From 12484b561a34e538e9a1f7491b2a9e0d0c00f098 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 7 Nov 2014 12:48:31 +1300 Subject: [PATCH 001/818] Initial (very unedited) commit for I-TASSER 4.0 --- .../easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb new file mode 100644 index 0000000000..41ca90e85b --- /dev/null +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -0,0 +1,29 @@ +easyblock = "PackedBinary" + +name = "I-TASSER" +version = '4.0' + +homepage = 'http://zhanglab.ccmb.med.umich.edu/I-TASSER/' +description = """I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function +modelling and comparison.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] + +dependencies = [] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + \ + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ + ['orca', 'otool_cosmo'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 95e649835e35b069c7068b4cc38abb90a5034ec8 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 1 Dec 2014 14:40:01 +1300 Subject: [PATCH 002/818] New Easyconfigs for I-TASSER 4.0 and 4.2 --- .../easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 25 ++++++++--------- .../easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 28 +++++++++++++++++++ 2 files changed, 40 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 41ca90e85b..23cb1b8f0c 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -9,21 +9,20 @@ modelling and comparison.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] +# Can't download from the web site as the file is behind a rego wall. +# The URL is, nevertheless, included here for reference. +#source_urls = ['http://zhanglab.ccmb.med.umich.edu/cgi-bin/download_I-TASSER.cgi?ID=358515010=I-TASSER%(version)s.tar.bz2'] +sources = ['%(name)s%(version)s.tar.bz2'] +patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [] +dependencies = [('BLAST', '2.2.29', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] + +postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], - 'dirs': [], + 'files': ['submitI-TASSER', 'I-TASSERmod/runI-TASSER.pl'], + 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'] } -moduleclass = 'chem' +moduleclass = 'bio' +modextravars = { 'IMINTASSERDB' : '/share/db/I-TASSER/%(version)s' } diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb new file mode 100644 index 0000000000..f3da26c72c --- /dev/null +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -0,0 +1,28 @@ +easyblock = "PackedBinary" + +name = "I-TASSER" +version = '4.2' + +homepage = 'http://zhanglab.ccmb.med.umich.edu/I-TASSER/' +description = """I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function +modelling and comparison.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Can't download from the web site as the file is behind a rego wall. +# The URL is, nevertheless, included here for reference. +#source_urls = ['http://zhanglab.ccmb.med.umich.edu/cgi-bin/download_I-TASSER.cgi?ID=358515010=I-TASSER%(version)s.tar.bz2'] +sources = ['%(name)s%(version)s.tar.bz2'] +patches = ['%(name)s-%(version)s-local-mods.patch'] + +dependencies = [('BLAST', '2.2.29', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] + +postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] + +sanity_check_paths = { + 'files': ['submitI-TASSER', 'I-TASSERmod/runI-TASSER.pl'], + 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'] +} + +moduleclass = 'bio' +modextravars = { 'IMINTASSERDB' : '/share/db/I-TASSER/%(version)s' } -- GitLab From 604f9b49733fd4f4a45646a3eb2c3eaaf4b2b87e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 18 Mar 2015 10:11:12 +1300 Subject: [PATCH 003/818] Downgraded BLAST from 2.2.29 to 2.2.26 --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 23cb1b8f0c..23b0318dd6 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(name)s%(version)s.tar.bz2'] patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [('BLAST', '2.2.29', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index f3da26c72c..519e1f06e3 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(name)s%(version)s.tar.bz2'] patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [('BLAST', '2.2.29', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] -- GitLab From 7b60524366b2aca23116214ba45d497129d50aa2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 18 Mar 2015 10:16:43 +1300 Subject: [PATCH 004/818] Removed BLAST toolchain specification --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 23b0318dd6..f9613f6727 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(name)s%(version)s.tar.bz2'] patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [('BLAST', '2.2.26', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26'), ('Java', '1.7.0_51')] postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 519e1f06e3..80f62bd20b 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(name)s%(version)s.tar.bz2'] patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [('BLAST', '2.2.26', '', ('ictce', '5.4.0')), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26'), ('Java', '1.7.0_51')] postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] -- GitLab From 88c902c61c93abfa97208bff78124d0d12ca000f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 18 Mar 2015 11:34:09 +1300 Subject: [PATCH 005/818] Added minor BLAST revision number --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index f9613f6727..1434110104 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(name)s%(version)s.tar.bz2'] patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [('BLAST', '2.2.26'), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 80f62bd20b..228054aadf 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(name)s%(version)s.tar.bz2'] patches = ['%(name)s-%(version)s-local-mods.patch'] -dependencies = [('BLAST', '2.2.26'), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] -- GitLab From bac2fa921a4790787d2804967276f43c23af7495 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 25 Jun 2015 17:44:36 +0200 Subject: [PATCH 006/818] NLopt easyconfig --- .../n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..abf5bbc277 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' -- GitLab From ed1dc57c34f1545070e4342fda5de040fa88636c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 13:57:11 +1300 Subject: [PATCH 007/818] Updates to extensions --- .../p/Python/Python-2.7.11-foss-2015a.eb | 89 +++++++++++++++++-- 1 file changed, 82 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 34c45f4ac7..17fa65688e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -8,7 +8,7 @@ description = """Python is a programming language that lets you work more quickl toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.10.1' +numpyversion = '1.10.2' scipyversion = '0.16.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] @@ -32,10 +32,10 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 exts_list = [ - ('setuptools', '18.7.1', { + ('setuptools', '20.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '7.1.2', { + ('pip', '8.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { @@ -51,7 +51,7 @@ exts_list = [ ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), - ('mpi4py', '1.3.1', { + ('mpi4py', '2.0.0', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { @@ -60,7 +60,7 @@ exts_list = [ ('argparse', '1.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), - ('pbr', '1.8.1', { + ('pbr', '0.11.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.12.2', { @@ -80,7 +80,7 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), - ('decorator', '4.0.4', { + ('decorator', '4.0.9', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), ('arff', '2.1.0', { @@ -97,7 +97,7 @@ exts_list = [ ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), - ('pyparsing', '2.0.6', { + ('pyparsing', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('netifaces', '0.10.4', { @@ -127,5 +127,80 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), ] + # The following are optional packages that we may or may not see fit to + # include. + # + #('astroid', '1.4.4', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/a/astroid'], + #}), + #('Fiona', '1.6.3', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/F/Fiona'], + #}), + #('h5py', '2.5.0', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/h/h5py'], + #}), + #('Jinja2', '2.8', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + #}), + #('line_profiler', '1.0', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/l/line_profiler'], + #}), + #('llvmlite', '0.8.0', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite'], + #}), + #('llvmmath', '0.1.1', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/l/llvmmath'], + #}), + #('llvmpy', '0.12.7', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/l/llvmpy'], + #}), + #('logilab-common', '1.1.0', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/l/logilab-common'], + #}), + #('MarkupSafe', '0.23', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe'], + #}), + #('matplotlib', '1.5.1', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + #}), + #('memory_profiler', '0.41', { + # 'source_tmpl': '%(name)s-%(version)s.tar.gz', + # 'source_urls': ['https://pypi.python.org/packages/source/m/memory_profiler'], + #}), + #('numba', '0.23.1', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/n/numba'], + #}), + #('numexpr', '2.5', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr'], + #}), + #('patsy', '0.4.1', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + #}), + #('prettytable', '0.7.2', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/p/prettytable'], + #}), + #('psutil', '4.0.0', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + #}), + #('psycopg2', '2.6.1', { + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'source_urls': ['https://pypi.python.org/packages/source/p/psycopg2'], + #}), moduleclass = 'lang' -- GitLab From f90562e072b4a88ab13fea299e890c8040f91048 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 30 Mar 2016 17:11:05 +1300 Subject: [PATCH 008/818] New easyconfig for Python 3 for FOSS 2015a --- .../p/Python/Python-3.5.1-foss-2015a.eb | 115 ++++++++++++++++++ 1 file changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb new file mode 100644 index 0000000000..9629fd32d4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '3.5.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.2' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.10.0'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Feb 25th 2016 +exts_list = [ + ('setuptools', '20.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + }), + ('scipy', scipyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' -- GitLab From fa58580a725e58f6aab7c741d9558cae9e6d2f3d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 6 Apr 2016 11:36:23 +1200 Subject: [PATCH 009/818] Updates to package versions --- .../p/Python/Python-2.7.11-foss-2015a.eb | 103 +++--------------- .../p/Python/Python-3.5.1-foss-2015a.eb | 30 +++-- 2 files changed, 34 insertions(+), 99 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 552cdc8882..a5514e370f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -8,8 +8,8 @@ description = """Python is a programming language that lets you work more quickl toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.10.2' -scipyversion = '0.16.1' +numpyversion = '1.11.0' +scipyversion = '0.17.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -23,19 +23,19 @@ dependencies = [ ('SQLite', '3.10.0'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), # required for pycrypto - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# package versions updated May 28th 2015 +# package versions updated 1 April 2016 exts_list = [ - ('setuptools', '20.1.1', { + ('setuptools', '20.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '8.0.2', { + ('pip', '8.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { @@ -60,19 +60,19 @@ exts_list = [ ('argparse', '1.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), - ('pbr', '0.11.1', { + ('pbr', '1.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.12.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.23.4', { + ('Cython', '0.24b0', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.4.2', { + ('dateutil', '2.5.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), @@ -97,7 +97,7 @@ exts_list = [ ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), - ('pyparsing', '2.1.0', { + ('pyparsing', '2.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('netifaces', '0.10.4', { @@ -112,10 +112,10 @@ exts_list = [ ('mock', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], }), - ('pytz', '2015.7', { + ('pytz', '2016.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), - ('pandas', '0.17.1', { + ('pandas', '0.18.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), ('enum34', '1.1.2', { @@ -126,84 +126,9 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), - ('virtualenv', '14.0.5', { + ('virtualenv', '15.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), ] - # The following are optional packages that we may or may not see fit to - # include. - # - #('astroid', '1.4.4', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/a/astroid'], - #}), - #('Fiona', '1.6.3', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/F/Fiona'], - #}), - #('h5py', '2.5.0', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/h/h5py'], - #}), - #('Jinja2', '2.8', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - #}), - #('line_profiler', '1.0', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/l/line_profiler'], - #}), - #('llvmlite', '0.8.0', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite'], - #}), - #('llvmmath', '0.1.1', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/l/llvmmath'], - #}), - #('llvmpy', '0.12.7', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/l/llvmpy'], - #}), - #('logilab-common', '1.1.0', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/l/logilab-common'], - #}), - #('MarkupSafe', '0.23', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe'], - #}), - #('matplotlib', '1.5.1', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - #}), - #('memory_profiler', '0.41', { - # 'source_tmpl': '%(name)s-%(version)s.tar.gz', - # 'source_urls': ['https://pypi.python.org/packages/source/m/memory_profiler'], - #}), - #('numba', '0.23.1', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/n/numba'], - #}), - #('numexpr', '2.5', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr'], - #}), - #('patsy', '0.4.1', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], - #}), - #('prettytable', '0.7.2', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/p/prettytable'], - #}), - #('psutil', '4.0.0', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], - #}), - #('psycopg2', '2.6.1', { - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'source_urls': ['https://pypi.python.org/packages/source/p/psycopg2'], - #}), moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 9629fd32d4..020cd82ccf 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -7,8 +7,8 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.10.2' -scipyversion = '0.16.1' +numpyversion = '1.11.0' +scipyversion = '0.17.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -29,12 +29,12 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! -# package versions updated Feb 25th 2016 +# package versions updated 1 April 2016 exts_list = [ - ('setuptools', '20.1.1', { + ('setuptools', '20.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '8.0.2', { + ('pip', '8.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { @@ -64,13 +64,13 @@ exts_list = [ ('lockfile', '0.12.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.23.4', { + ('Cython', '0.24b0', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.4.2', { + ('dateutil', '2.5.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), @@ -97,8 +97,8 @@ exts_list = [ }), ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.1.0', { + }), + ('pyparsing', '2.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('netifaces', '0.10.4', { @@ -107,9 +107,19 @@ exts_list = [ ('netaddr', '0.7.18', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), - ('pandas', '0.17.1', { + ('pytz', '2016.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.18.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' -- GitLab From 2061c62eeefb657ee1277f35be7c104c4b454159 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 6 Apr 2016 14:36:27 +1200 Subject: [PATCH 010/818] Revert NumPy version --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index a5514e370f..2a7f187bad 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -8,7 +8,7 @@ description = """Python is a programming language that lets you work more quickl toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.11.0' +numpyversion = '1.10.1' scipyversion = '0.17.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 020cd82ccf..d5d4531b05 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -7,7 +7,7 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.11.0' +numpyversion = '1.10.1' scipyversion = '0.17.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -- GitLab From 9aaf9d0a12434b5c4ded1efa5c2eaced92d26643 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 17 May 2016 11:37:05 +1200 Subject: [PATCH 011/818] Clarified some comments and took out a local patch --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 3 +-- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 1434110104..2a1ad2658f 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -9,11 +9,10 @@ modelling and comparison.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -# Can't download from the web site as the file is behind a rego wall. +# Can't download from the web site automatically as registration is required. # The URL is, nevertheless, included here for reference. #source_urls = ['http://zhanglab.ccmb.med.umich.edu/cgi-bin/download_I-TASSER.cgi?ID=358515010=I-TASSER%(version)s.tar.bz2'] sources = ['%(name)s%(version)s.tar.bz2'] -patches = ['%(name)s-%(version)s-local-mods.patch'] dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 228054aadf..02e174bf10 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -9,11 +9,10 @@ modelling and comparison.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -# Can't download from the web site as the file is behind a rego wall. +# Can't download from the web site automatically as registration is required. # The URL is, nevertheless, included here for reference. #source_urls = ['http://zhanglab.ccmb.med.umich.edu/cgi-bin/download_I-TASSER.cgi?ID=358515010=I-TASSER%(version)s.tar.bz2'] sources = ['%(name)s%(version)s.tar.bz2'] -patches = ['%(name)s-%(version)s-local-mods.patch'] dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] -- GitLab From 542a11b6a741ec72a256e924441d259b0a273846 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 21 Jun 2016 14:03:12 +1200 Subject: [PATCH 012/818] Update homepage and description --- .../m/muParser/muParser-2.2.5-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.2.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-foss-2015a.eb b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-foss-2015a.eb new file mode 100644 index 0000000000..2145d8a94c --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'muParser' +version = '2.2.5' + +homepage = 'http://beltoforion.de/article.php?a=muparser' +description = """muParser is an extensible high performance math expression +parser library written in C++. It works by transforming a mathematical +expression into bytecode and precalculating constant parts of the expression.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://github.com/beltoforion/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +configopts = "--disable-samples --enable-shared" + +sanity_check_paths = { + 'files': ['lib/libmuparser.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'math' -- GitLab From 1a95b45eb1f3e6281a785be97fde788a786ba573 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 21 Jun 2016 15:43:11 +1200 Subject: [PATCH 013/818] New EasyConfig for Xerces-C++ 3.1.3 with the foss-2015a toolchain --- .../Xerces-C++/Xerces-C++-3.1.3-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.3-foss-2015a.eb new file mode 100644 index 0000000000..6b2b631d51 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.3' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' +] + +dependencies = [ + ('cURL', '7.46.0'), +] + +moduleclass = 'lib' -- GitLab From 6f9fc944a4a120b8c2d276e6af92d97af3887d8a Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 10 Aug 2016 18:53:28 -0500 Subject: [PATCH 014/818] Adding an Easyconfig for Connectome Workbench --- .../ConnectomeWorkbench-1.2.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb new file mode 100644 index 0000000000..2be243b7e0 --- /dev/null +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'ConnectomeWorkbench' +version = '1.2.2' + +homepage = 'http://www.humanconnectome.org/software/get-connectome-workbench.html' +description = """Connectome Workbench is an open-source +visualization and discovery tool used to explore data generated +by the Human Connectome Project. The distribution includes wb_view, +a GUI-based visualization platform, and wb_command, a command-line +program for performing a variety of algorithmic tasks using volume, +surface, and grayordinate data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://ftp.humanconnectome.org/workbench/'] +sources = ['workbench-rh_linux64-v%(version)s.zip'] + +modextrapaths = {'PATH': 'bin_rh_linux64', 'LIBRARY_PATH': 'libs_rh_linux64', +'LD_LIBRARY_PATH': 'libs_rh_linux64'} + +sanity_check_paths = { + 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", + "bin_rh_linux64/wb_view",], + 'dirs': ["resources"] +} + +moduleclass = 'bio' + -- GitLab From b5ea364f85f293337f3ffad1446543c3b9869863 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 9 Sep 2016 22:09:31 +1200 Subject: [PATCH 015/818] Minor changes per suggestions from K.H. --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 5 ++--- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 2a1ad2658f..4ab6203c78 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -10,13 +10,12 @@ modelling and comparison.""" toolchain = {'name': 'dummy', 'version': 'dummy'} # Can't download from the web site automatically as registration is required. -# The URL is, nevertheless, included here for reference. -#source_urls = ['http://zhanglab.ccmb.med.umich.edu/cgi-bin/download_I-TASSER.cgi?ID=358515010=I-TASSER%(version)s.tar.bz2'] +# The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. sources = ['%(name)s%(version)s.tar.bz2'] dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] -postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] +postinstallcmds = ['chmod a+x %(installdir)s/submit%(name)s'] sanity_check_paths = { 'files': ['submitI-TASSER', 'I-TASSERmod/runI-TASSER.pl'], diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 02e174bf10..6ce5db2685 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -10,13 +10,12 @@ modelling and comparison.""" toolchain = {'name': 'dummy', 'version': 'dummy'} # Can't download from the web site automatically as registration is required. -# The URL is, nevertheless, included here for reference. -#source_urls = ['http://zhanglab.ccmb.med.umich.edu/cgi-bin/download_I-TASSER.cgi?ID=358515010=I-TASSER%(version)s.tar.bz2'] +# The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. sources = ['%(name)s%(version)s.tar.bz2'] dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] -postinstallcmds = ['/bin/chmod +x %(installdir)s/submit%(name)s'] +postinstallcmds = ['chmod a+x %(installdir)s/submit%(name)s'] sanity_check_paths = { 'files': ['submitI-TASSER', 'I-TASSERmod/runI-TASSER.pl'], -- GitLab From 6b65c160cd0255f2bd123e04c591470efe52aa83 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 9 Sep 2016 22:12:36 +1200 Subject: [PATCH 016/818] Update version of Java --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 4ab6203c78..c92177166e 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. sources = ['%(name)s%(version)s.tar.bz2'] -dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_80')] postinstallcmds = ['chmod a+x %(installdir)s/submit%(name)s'] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 6ce5db2685..93f184aa24 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. sources = ['%(name)s%(version)s.tar.bz2'] -dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_51')] +dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_80')] postinstallcmds = ['chmod a+x %(installdir)s/submit%(name)s'] -- GitLab From a5b2984c569ffdebc1a7d7cb886b439631334e46 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:25:38 +0200 Subject: [PATCH 017/818] add easyconfig MultiQC-0.7-goolf-1.7.20.eb --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb new file mode 100644 index 0000000000..1d864fa9f0 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -0,0 +1,79 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'MultiQC' +version = '0.7' + +homepage = 'http://multiqc.info/' +description = """Aggregate results from bioinformatics analyses across many samples into a single report""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': False, 'pic': False} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s'), + ('numpy', '1.10.1', '-Python-%(pyver)s'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('pyparsing', '2.1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('pytz', '2016.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + }), + ('python-dateutil', '2.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('PyYAML', '3.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('multiqc', version, { + #'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], + 'LD_LIBRARY_PATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_paths = { + 'files': [], + #'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] + 'dirs': ['.'] +} + +moduleclass = 'bio' -- GitLab From 4d84d1c074fd1ce8e38af2ffb9df37698abb7bd2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:34:56 +0200 Subject: [PATCH 018/818] added missing deps --- ...lotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb | 45 +++++++++++++++++++ ...numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb | 23 ++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..506dad104c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.5.5'), + ('libpng', '1.6.18'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..b4a5ec30e9 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +#patches = ['numpy-1.8.0-mkl.patch'] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' -- GitLab From 1692d120c89603830a89dac9eb2348d6d1d0f2bf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:43:45 +0200 Subject: [PATCH 019/818] added sanity checking --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 1d864fa9f0..7c5179be13 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -71,9 +71,8 @@ modextrapaths = { } sanity_check_paths = { - 'files': [], - #'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] - 'dirs': ['.'] + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/multiqc-%(version)s-py%(pyshortver)s.egg'] } moduleclass = 'bio' -- GitLab From ad9690f939d7cb1df29891addb2e6ab2bd943116 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:57:10 +0200 Subject: [PATCH 020/818] added missing deps --- .../f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.18-goolf-1.7.20.eb | 19 +++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb new file mode 100644 index 0000000000..c3aab419f3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.18')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb new file mode 100644 index 0000000000..a083925f91 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.18' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From 8ade81939c72f037ae59f9f4e7f1f2d16d478740 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 08:58:56 +0200 Subject: [PATCH 021/818] remove toolchainopts --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 7c5179be13..3c54d448e9 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -12,7 +12,6 @@ homepage = 'http://multiqc.info/' description = """Aggregate results from bioinformatics analyses across many samples into a single report""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': False, 'pic': False} parallel = 1 -- GitLab From 516ee8e6c960b2723c9dbb4d86465de772ce7c52 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:00:14 +0200 Subject: [PATCH 022/818] remove numpy dep --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 3c54d448e9..f2c87048d9 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -18,7 +18,7 @@ parallel = 1 dependencies = [ ('Python', '2.7.11'), ('matplotlib', '1.5.1', '-Python-%(pyver)s'), - ('numpy', '1.10.1', '-Python-%(pyver)s'), + # numpy dependency provided by python module ] # this is a bundle of Python packages -- GitLab From 7680debb5c3e01b70ca6fe8e1fd8bfc2572248c8 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:00:43 +0200 Subject: [PATCH 023/818] added version suffix --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index f2c87048d9..14c2e7f378 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -7,6 +7,7 @@ easyblock = 'Bundle' name = 'MultiQC' version = '0.7' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://multiqc.info/' description = """Aggregate results from bioinformatics analyses across many samples into a single report""" -- GitLab From 264450f3c354dc0d322b16b8e4eaa1348b3288ce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:23:45 +0200 Subject: [PATCH 024/818] file renamed to add suffix --- ...-goolf-1.7.20.eb => MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MultiQC/{MultiQC-0.7-goolf-1.7.20.eb => MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb rename to easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb -- GitLab From 7c1c632123eea66191c8bb8a4a75218f8621dadf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 15:24:30 +0200 Subject: [PATCH 025/818] updated dependencies --- .../f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.21-goolf-1.7.20.eb | 19 +++++++++++++++++ ...lotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb | 4 ++-- 3 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..76cd412cf3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb new file mode 100644 index 0000000000..cb4fbebab2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb index 506dad104c..697a58300b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb @@ -16,8 +16,8 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.11'), - ('freetype', '2.5.5'), - ('libpng', '1.6.18'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), ] exts_list = [ -- GitLab From c9deaf559758da992ec9deb41ad0786a176644b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Oct 2016 16:11:19 +0200 Subject: [PATCH 026/818] add easyconfig Boost-1.62.0-intel-2016b-Python-2.7.12.eb --- .../Boost-1.62.0-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8f21675328 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.62.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 19ece4eea21398f809056a138dbb6bc14abc5eca Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 11 Oct 2016 15:07:45 +0200 Subject: [PATCH 027/818] Caffe rc3 built using the foss 2016a toolchain. --- ...6a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb new file mode 100644 index 0000000000..9a164bb75c --- /dev/null +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'Caffe' +version = 'rc3' + +cudaversion = '7.5.18' +versionsuffix = '-CUDA-%s-Python-%%(pyver)s' % cudaversion + +homepage = 'https://github.com/BVLC/caffe' +description = """ +Caffe is a deep learning framework made with expression, speed, +and modularity in mind. It is developed by the Berkeley Vision +and Learning Center (BVLC) and community contributors. +""" +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': False, 'pic': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/BVLC/caffe/archive/'] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +protobuf_ver = '3.0.2' + +dependencies = [ + ('glog', '0.3.4'), + ('gflags', '2.1.2'), + ('OpenCV', '3.1.0'), + ('CUDA', cudaversion, '', True), + ('cuDNN', '4.0', '', True), + ('LMDB', '0.9.18'), + ('LevelDB', '1.18'), + ('snappy', '1.1.3'), + ('protobuf', protobuf_ver), + ('protobuf-python', protobuf_ver, '-Python-%(pyver)s'), + ('HDF5', '1.8.16', '-serial'), + ('Boost', '1.61.0', '-Python-%(pyver)s'), + ('Python', '2.7.11'), + ('scikit-image', '0.12.3', '-Python-%(pyver)s') +] + +configopts = '-DBLAS=open' + +modextrapaths = {'PYTHONPATH': ['python'] } + +sanity_check_paths = { + 'files': ['bin/caffe'] + + ['lib/%s' % x for x in ['libcaffe.so','libproto.a']] + + ['python/caffe/_caffe.so'] + + ['include/caffe/proto/caffe.pb.h'], + 'dirs': [], +} + +sanity_check_commands = [('python', "-c 'import caffe'")] + +moduleclass = 'devel' -- GitLab From 0ea09aa90e2af9b75352003f330c838a7a52c1fc Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 11 Oct 2016 15:23:33 +0200 Subject: [PATCH 028/818] Fixed filename, which accidentally included foss-2016a twice. --- ...2016a.eb => Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/Caffe/{Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb => Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb rename to easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb -- GitLab From 15d394c14be18599f491510d34ffb865316eddb2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 6 Nov 2016 12:03:45 +0100 Subject: [PATCH 029/818] HDF5 has a dependency on libxml2 --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index 84580d9ba8..c0d4209263 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -21,6 +21,7 @@ buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), + ('libxml2', '2.9.4') ] moduleclass = 'data' -- GitLab From e3823e59665b2f2fa750e44b6164b58e67f72942 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 6 Nov 2016 13:29:13 +0100 Subject: [PATCH 030/818] version conflict --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index c0d4209263..7250d32fe5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -21,7 +21,7 @@ buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), - ('libxml2', '2.9.4') + ('libxml2', '2.9.3') ] moduleclass = 'data' -- GitLab From 3e52fe9b81e7626776436ac19923e55bb92b7a06 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 14 Nov 2016 10:38:30 +0100 Subject: [PATCH 031/818] versionsuffix removed for mentioned easyconfigs --- .../l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb | 2 +- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb index dc2d40a915..7498899794 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.47.0'), - ('libxml2', '2.9.3', versionsuffix), + ('libxml2', '2.9.3'), ('LibUUID', '1.0.3'), ] diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 111f00bfda..de510f4adc 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -17,7 +17,7 @@ dependencies = [ ('Java', '1.7.0_79', '', True), ('Python', '2.7.11'), ('HDF5', '1.8.16'), - ('libxml2', '2.9.3', '-Python-%(pyver)s'), + ('libxml2', '2.9.3'), ('zlib', '1.2.8') ] -- GitLab From e3c946a324d60d3e0f738a738d44cd0e4c470fac Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 14 Nov 2016 10:58:16 +0100 Subject: [PATCH 032/818] without versionsuffix --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index 7250d32fe5..b1098f85e1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -24,4 +24,4 @@ dependencies = [ ('libxml2', '2.9.3') ] -moduleclass = 'data' +moduleclass = 'data' \ No newline at end of file -- GitLab From 90f2128e2f159b44e8cbc0dc9173014304a3b9c0 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 16 Nov 2016 15:55:39 +0200 Subject: [PATCH 033/818] adding easyconfigs: CP2K-4.1-foss-2016b-psmp.eb --- .../b/byacc/byacc-20160606-foss-2016b.eb | 22 ++++++++ .../c/CP2K/CP2K-4.1-foss-2016b-psmp.eb | 54 +++++++++++++++++++ .../easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb | 19 +++++++ .../g/Guile/Guile-1.8.8-foss-2016b.eb | 32 +++++++++++ .../l/Libint/Libint-1.1.6-foss-2016b.eb | 27 ++++++++++ .../libmatheval-1.1.11-foss-2016b.eb | 33 ++++++++++++ .../libunistring-0.9.6-foss-2016b.eb | 24 +++++++++ .../l/libxc/libxc-2.2.3-foss-2016b.eb | 31 +++++++++++ .../l/libxsmm/libxsmm-1.4.4-foss-2016b.eb | 26 +++++++++ .../p/PLUMED/PLUMED-2.2.3-foss-2016b.eb | 42 +++++++++++++++ 10 files changed, 310 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20160606-foss-2016b.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20160606-foss-2016b.eb b/easybuild/easyconfigs/b/byacc/byacc-20160606-foss-2016b.eb new file mode 100644 index 0000000000..93c0899ae1 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160606-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160606' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['d527c811b360f04a8c5f5a0a90625966'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb new file mode 100644 index 0000000000..85ce41dbb8 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb @@ -0,0 +1,54 @@ +name = 'CP2K' +version = '4.1' +versionsuffix = '-psmp' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ +# 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '2.2.3'), + ('PLUMED', '2.2.3'), + ('libxsmm', '1.4.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] +# Don't run tests, they use mpirun +runtest = False + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +type = 'psmp' + +# regression test reports failures +ignore_regtest_fails = True + +plumed = True + +postinstallcmds = [ "cp -a %(builddir)s/%(namelower)s-%(version)s/data %(installdir)s" ] + +modextravars = { + 'CP2K_DATA_DIR': '%(installdir)s/data', +} + + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb new file mode 100644 index 0000000000..74ae6cc390 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = "2.1" + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'version': '2016b', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016b.eb new file mode 100644 index 0000000000..dce576ef30 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.1'), + ('libunistring', '0.9.6'), + ('pkg-config', '0.29.1'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb new file mode 100644 index 0000000000..08a7cf496f --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb @@ -0,0 +1,27 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +source_urls = ['https://github.com/evaleev/libint/archive/'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb new file mode 100644 index 0000000000..187e735268 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160606'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2016b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2016b.eb new file mode 100644 index 0000000000..9d6b0fbbc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.6' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb new file mode 100644 index 0000000000..969028930d --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-foss-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-foss-2016b.eb new file mode 100644 index 0000000000..f4d92dd6cb --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-foss-2016b.eb new file mode 100644 index 0000000000..cefea54afb --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-foss-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.3' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From d5d900f575dd82f4826eacd62a5d0fc2d174f254 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 29 Nov 2016 17:49:59 +0100 Subject: [PATCH 034/818] adding easyconfigs: QIIME-1.9.1.eb --- easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb | 29 ++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb diff --git a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb new file mode 100644 index 0000000000..d51a7c6584 --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Conda' + +name = "QIIME" +version = "1.9.1" +variant = "Linux-x86_64" + +homepage = 'http://qiime.org/' +description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.""" + +toolchain = {'name': 'dummy', 'version': ''} + +requirements = "python=2.7 %(namelower)s=%(version)s matplotlib=1.4.3 mock nose" +channels = ['bioconda'] + +builddependencies = [('Anaconda2', '4.0.0')] + +sanity_check_paths = { + 'files': ['bin/print_qiime_config.py'], + 'dirs': [] +} + +sanity_check_commands = ['print_qiime_config.py -t'] + +moduleclass = 'bio' -- GitLab From 51bb3205862ddc74ce078b6c1355974ccf0722c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Dec 2016 15:53:30 +0100 Subject: [PATCH 035/818] adding easyconfigs: CP2K-4.1-intel-2016b.eb, libxsmm-1.6-intel-2016b.eb --- .../c/CP2K/CP2K-4.1-intel-2016b.eb | 41 +++++++++++++++++++ .../l/libxsmm/libxsmm-1.6-intel-2016b.eb | 26 ++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb new file mode 100644 index 0000000000..cd0f3a9a66 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb @@ -0,0 +1,41 @@ +name = 'CP2K' +version = '4.1' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '2.2.3'), + ('PLUMED', '2.2.3'), + ('libxsmm', '1.6'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +plumed = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb new file mode 100644 index 0000000000..bb0cffc7fe --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.6' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' -- GitLab From 7727f04619ae6d324ad7f1de524ffa9f944f3530 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 19 Dec 2016 11:26:11 +1300 Subject: [PATCH 036/818] New EasyConfig for NetLogo --- .../easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb new file mode 100644 index 0000000000..fa15b824e3 --- /dev/null +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'NetLogo' +version = '5.3.1' +versionsuffix = '-64' + +homepage = 'http://ccl.northwestern.edu/netlogo/' +description = """NetLogo is a multi-agent programmable modeling environment. It +is used by tens of thousands of students, teachers and researchers worldwide. +It also powers HubNet participatory simulations. It is authored by Uri Wilensky +and developed at the CCL.""" + +# NetLogo needs Java, but no particular toolchain +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] + +# If the suffix (e.g., bits) is present in the expanded tarball, remove it. +#unpack_options = "--transform='s,^%(namelower)s-%(version)s%(versionsuffix)s,%(namelower)s-%(version)s,'" + +dependencies = [ + ('Java', '1.8.0_40') +] + +sanity_check_paths = { + 'files': ['NetLogo', 'NetLogo3D', 'NetLogoLogging'], + 'dirs': ['app', 'runtime'], +} + +moduleclass = 'math' -- GitLab From 8a35310c3eef9e1d5329b0f600be18cff20692d1 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 19 Dec 2016 11:28:12 +1300 Subject: [PATCH 037/818] Don't bother transforming the extracted src dir --- easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb index fa15b824e3..1869d96297 100644 --- a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb @@ -16,9 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] -# If the suffix (e.g., bits) is present in the expanded tarball, remove it. -#unpack_options = "--transform='s,^%(namelower)s-%(version)s%(versionsuffix)s,%(namelower)s-%(version)s,'" - dependencies = [ ('Java', '1.8.0_40') ] -- GitLab From 652909b293ea91e488aefc98dbddf8e374569a40 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 19 Dec 2016 11:32:35 +1300 Subject: [PATCH 038/818] NetLogo comes with its own Java - therefore no dependencies --- easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb index 1869d96297..bd778d69d8 100644 --- a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb @@ -10,16 +10,13 @@ is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL.""" -# NetLogo needs Java, but no particular toolchain +# NetLogo is precompiled and needs no particular toolchain. +# It even comes with its own Java. toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] -dependencies = [ - ('Java', '1.8.0_40') -] - sanity_check_paths = { 'files': ['NetLogo', 'NetLogo3D', 'NetLogoLogging'], 'dirs': ['app', 'runtime'], -- GitLab From d34bc662b812b57f520cc8870fb7b2a1393b53c0 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 20 Dec 2016 12:02:58 +0100 Subject: [PATCH 039/818] adding easyconfigs: Minia-2.0.7-goolf-1.7.20.eb --- .../m/Minia/Minia-2.0.7-goolf-1.7.20.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb new file mode 100644 index 0000000000..8523144221 --- /dev/null +++ b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'Minia' +version = '2.0.7' + +homepage = 'http://minia.genouest.org/' +description = """Minia is a short-read assembler based on a de Bruijn graph""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/GATB/minia/releases/download/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s-Source.tar.gz'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [('zlib', '1.2.8')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/minia"], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 46e2a74612f995049c41f42e5a0321b93bd64ad1 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 21 Dec 2016 12:41:01 +0100 Subject: [PATCH 040/818] added missing cmake easyconfig --- .../c/CMake/CMake-3.4.3-goolf-1.7.20.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..383be7ac07 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 06b3f5dbc9df4fb041f2d556a33105479c3fe85a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Dec 2016 12:20:15 +0100 Subject: [PATCH 041/818] adding easyconfigs: EasyBuild-3.0.2.eb --- .../e/EasyBuild/EasyBuild-3.0.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb new file mode 100644 index 0000000000..708295ab3c --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.0.2' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/aa/d9/7dc5b88a5644975683b4df1d0a16be90f6af4598528aa68dba27f7f3c532', + # vsc-base + 'https://pypi.python.org/packages/73/24/e4244a743e0cfc4af1f3b3b772698e2f4dafc7052bc006a1b829b66f7a3a', + # easybuild-framework + 'https://pypi.python.org/packages/b3/cd/d9720621804e083e2ef7ffa4a746f011933a4f1314d6d34e871517d3cb5c', + # easybuild-easyblocks + 'https://pypi.python.org/packages/6e/b8/77f635112bb78799195e31053d3827e86c07c635ac9ac03d691d7fc6f655', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/05/92/c39b8430f27a028d7c9065ad80639c15c5f11844012801937e24435a262f', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.21.tar.gz', + 'vsc-base-2.5.5.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From f7d2a6301a6361eebeef69b1c1cc190f590e73a3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Dec 2016 14:15:05 +0000 Subject: [PATCH 042/818] Update GSL to 2.3 for foss-2016b --- .../easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb new file mode 100644 index 0000000000..35f4331406 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'version': '2016b', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--with-pic' + +moduleclass = 'numlib' -- GitLab From 14d63fa65ccf60fe9df28d560aebdb5961fa957a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Dec 2016 14:20:08 +0000 Subject: [PATCH 043/818] Update EIGENSORT to 6.1.4 for foss-2016b --- .../e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb new file mode 100644 index 0000000000..5b6b65198e --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 6.1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +# Provided binaries required OpenBLAS and GSL libraries + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '6.1.4' + +homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/' +] +sources = ['EIG-%(version)s.tar.gz'] + +dependencies = [ + ('GSL', '2.3'), +] + +# -lm and -pthread are missing in the Makefile +# also run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl $LIBBLAS -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' + +start_dir = 'src' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 4fc696c30669917e29f22d4d80c245ba1b42c754 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Dec 2016 14:21:16 +0000 Subject: [PATCH 044/818] Fix toolchain order --- easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb index 35f4331406..b5798d1552 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb @@ -8,7 +8,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" -toolchain = {'version': '2016b', 'name': 'foss'} +toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 52ec3b03afb70192a0b3958335d9342d44722532 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Dec 2016 18:20:42 +0000 Subject: [PATCH 045/818] Kraken for foss-2016b, plus deps --- .../Jellyfish/Jellyfish-1.1.11-foss-2016b.eb | 29 ++++++++++++ ...aken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 44 +++++++++++++++++++ .../l/libidn/libidn-1.32-foss-2016b.eb | 19 ++++++++ .../w/wget/wget-1.17.1-foss-2016b.eb | 40 +++++++++++++++++ 4 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016b.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb new file mode 100644 index 0000000000..6acf8320e7 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Foss-2016b version +# modified by: +# Adam Huffman +# The Francis Crick Institute +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.11' + +homepage = 'http://www.cbcb.umd.edu/software/jellyfish/' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cbcb.umd.edu/software/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..8814a7c92c --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '0.10.5-beta' +versionsuffix='-Perl-%(perlver)s' + +homepage = 'http://ccb.jhu.edu/software/kraken/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +#Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['http://ccb.jhu.edu/software/kraken/dl/'] +sources = [SOURCELOWER_TGZ] + +patches = ['Kraken_%(version)s_makefile.patch'] + +dependencies = [ + ('Perl', '5.24.0'), + ('Jellyfish', '1.1.11'), + ('wget', '1.17.1'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016b.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016b.eb new file mode 100644 index 0000000000..d505fd0deb --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016b.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016b.eb new file mode 100644 index 0000000000..10ef0d42d4 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.17.1' + +homepage = 'https://www.gnu.org/software/wget/' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('PCRE', '8.38'), + ('libidn', '1.32'), + ('zlib', '1.2.8'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1s'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.4.11'), +] + +configopts = '--with-ssl=openssl ' + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/wget'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 6c6f05da815195db82a0b9960cbb575dce53cc01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Jan 2017 18:46:15 +0100 Subject: [PATCH 046/818] adding easyconfigs: zlib-1.2.10.eb --- easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb new file mode 100644 index 0000000000..02bb809a0b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.10' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/'] +sources = [SOURCELOWER_TAR_GZ] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 6ec49b353f0b3f457afee3fc6382ed0e2cd7a440 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 27 Jul 2016 22:07:48 +0200 Subject: [PATCH 047/818] ENH: add easyconfig for WPS3.8 --- .../w/WPS/WPS-3.8-intel-2016a-dmpar.eb | 35 +++++++++++++++++++ .../w/WPS/WPS-3.8_fix_known_problems.patch | 28 +++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb new file mode 100644 index 0000000000..8ee829c884 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb @@ -0,0 +1,35 @@ +name = 'WPS' +version = '3.8' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True} + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +checksums = ['2ab4e4ddae4e105432c18c59819a4523'] + +patches = ['WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_fix_known_problems.patch'] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.2'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('JasPer', '1.900.1'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch b/easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch new file mode 100644 index 0000000000..e03a2fbc76 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch @@ -0,0 +1,28 @@ +--- WPS.orig/ungrib/src/rd_grib1.F 2013-06-08 00:48:10.000000000 +0200 ++++ WPS/ungrib/src/rd_grib1.F 2016-07-26 11:02:19.021497705 +0200 +@@ -406,7 +406,7 @@ + !print *,'new dx = ',map%dx + endif + endif +- if ( ABS((map%ny-1) * map%dy - 2.*abs(map%lat1)) .lt. 1 ) then ++ if ( ABS((map%ny-1) * map%dy - 2.*abs(map%lat1)) .lt. 1. ) then + if ( ABS ( map%dy - (2.*abs(map%lat1)/real(map%ny-1)) ) .gt. 0.00001 ) then + !print *,'old dy = ',ginfo(9) + map%dy = 2.*abs(map%lat1)/real(map%ny-1) +@@ -471,6 +471,16 @@ + map%lat1 = ginfo(3) + write(tmp8,'(b8.8)') infogrid(5) + if (tmp8(5:5) .eq. '0') map%grid_wind = .false. ++! If this is global data, then the dx and dy are more accurately ++! computed by the number of points than the 3 digits grib permits. ++ if ( ABS(map%nx * map%dx - 360.) .lt. 1. ) then ++ if ( ABS ( map%dx - (360./real(map%nx)) ) .gt. 0.00001 ) then ++ ! print *,'old dx = ',ginfo(8) ++ map%dx = 360./real(map%nx) ++ ! print *,'new dx = ',map%dx ++ endif ++ endif ++ + + elseif (ksec2(4).eq.5) then ! Polar-Stereographic Grid. + map%igrid = 5 -- GitLab From 8b44bad8fda472d2a58e14311618d726e9c731f2 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 27 Jul 2016 22:25:32 +0200 Subject: [PATCH 048/818] DOC: add comment about WPS known problems --- easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb index 8ee829c884..1b72f4dbcc 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb @@ -17,6 +17,8 @@ source_urls = [ checksums = ['2ab4e4ddae4e105432c18c59819a4523'] +# patches for known problems as of 27 Jul 2016, see +# http://www2.mmm.ucar.edu/wrf/users/wpsv3.8/known-prob-3.8.html patches = ['WPS-%(version)s_netCDF-Fortran_seperate_path.patch', 'WPS-%(version)s_fix_known_problems.patch'] -- GitLab From b4b41745a58a975734a514860606b6b68706cd47 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 17 Aug 2016 15:48:26 +0200 Subject: [PATCH 049/818] BUG: rename patch file --- ...rate_path.patch => WPS-3.8_netCDF-Fortran_seperate_path.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/WPS/{WPS_netCDF-Fortran_seperate_path.patch => WPS-3.8_netCDF-Fortran_seperate_path.patch} (100%) diff --git a/easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-3.8_netCDF-Fortran_seperate_path.patch similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch rename to easybuild/easyconfigs/w/WPS/WPS-3.8_netCDF-Fortran_seperate_path.patch -- GitLab From 1b41f2d29ce7f43ac6040e075b973f199c191be3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2016 22:52:56 +0100 Subject: [PATCH 050/818] restore original name of WPS patch file as it is used by other existing easyconfigs --- easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb | 6 ++++-- ...te_path.patch => WPS_netCDF-Fortran_seperate_path.patch} | 0 2 files changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/w/WPS/{WPS-3.8_netCDF-Fortran_seperate_path.patch => WPS_netCDF-Fortran_seperate_path.patch} (100%) diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb index 1b72f4dbcc..c426109e50 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb @@ -19,8 +19,10 @@ checksums = ['2ab4e4ddae4e105432c18c59819a4523'] # patches for known problems as of 27 Jul 2016, see # http://www2.mmm.ucar.edu/wrf/users/wpsv3.8/known-prob-3.8.html -patches = ['WPS-%(version)s_netCDF-Fortran_seperate_path.patch', - 'WPS-%(version)s_fix_known_problems.patch'] +patches = [ + 'WPS_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_fix_known_problems.patch', +] buildtype = "dmpar" versionsuffix = '-%s' % buildtype diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.8_netCDF-Fortran_seperate_path.patch rename to easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch -- GitLab From 663b1224cabaf0d494039dc95a0d443ddfd52c97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2017 14:34:18 +0100 Subject: [PATCH 051/818] adding easyconfigs: HPL-2.2-foss-2017a.eb --- .../b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb | 27 +++++++++ .../b/binutils/binutils-2.27-GCCcore-6.3.0.eb | 21 +++++++ .../f/FFTW/FFTW-3.3.5-gompi-2017a.eb | 35 ++++++++++++ .../f/flex/flex-2.6.3-GCCcore-6.3.0.eb | 24 ++++++++ easybuild/easyconfigs/f/foss/foss-2017a.eb | 35 ++++++++++++ easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb | 25 +++++++++ .../easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 54 ++++++++++++++++++ easybuild/easyconfigs/g/gompi/gompi-2017a.eb | 20 +++++++ .../easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb | 18 ++++++ .../help2man/help2man-1.47.4-GCCcore-6.3.0.eb | 24 ++++++++ .../h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb | 23 ++++++++ .../m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 28 ++++++++++ .../numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb | 23 ++++++++ ...BLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb | 55 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 33 +++++++++++ ...ompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb | 25 +++++++++ .../z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb | 25 +++++++++ 17 files changed, 495 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2017a.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2017a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..76ea1be843 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..27418ca0e7 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.27' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.10'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb new file mode 100644 index 0000000000..6975badd80 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +# FIXME +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..e7dd6de964 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/foss/foss-2017a.eb b/easybuild/easyconfigs/f/foss/foss-2017a.eb new file mode 100644 index 0000000000..58f252b974 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2017a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.3.0-2.27' + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.1' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '2.0.2', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.5', '', comp_mpi_tc), # FIXME: --enable-sse2 --enable-avx --enable-avx2 --enable-avx512 + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..93f922e6d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.3.0' + +binutilsver = '2.27' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb new file mode 100644 index 0000000000..725e558810 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '6.3.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.5' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.1.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.27'), +] + +patches = [ + ('mpfr-%s-allpatches-20161215.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + 'GCCcore-6.2.0-fix-find-isl.patch', +] + +checksums = [ + '677a7623c7ef6ab99881bc4e048debb6', # gcc-6.3.0.tar.bz2 + '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 + 'b1d23a55588e3b2a13e3be66bc69fd8d', # mpfr-3.1.5.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2017a.eb b/easybuild/easyconfigs/g/gompi/gompi-2017a.eb new file mode 100644 index 0000000000..7022e6111e --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2017a.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2017a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.3.0-2.27' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 6.3.0 and binutils 2.27 + ('OpenMPI', '2.0.2', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb new file mode 100644 index 0000000000..e59ac471b9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..4931b9f6ce --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..b130fe6456 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..ffbaa7a77a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..ee922f3337 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..94fc300c72 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..1676fb43ff --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +sources = ['openmpi-%(version)src2.tar.gz'] # FIXME + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..07590857f9 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '6.3.0-2.27'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..89be4a6599 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.10' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 3e71cd82e968afd26f38a8fc044145a938d0d045 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2017 15:18:48 +0100 Subject: [PATCH 052/818] adding easyconfigs: HPL-2.2-intel-2017a.eb, intel-2017a.eb, imkl-2017.1.132-iimpi-2017a.eb, iimpi-2017a.eb, impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb, iccifort-2017.1.132-GCC-6.3.0-2.27.eb, ifort-2017.1.132-GCC-6.3.0-2.27.eb, icc-2017.1.132-GCC-6.3.0-2.27.eb --- .../easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb | 18 +++++++++ .../i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb | 33 ++++++++++++++++ .../iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 18 +++++++++ .../ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb | 36 ++++++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb | 20 ++++++++++ .../i/imkl/imkl-2017.1.132-iimpi-2017a.eb | 38 +++++++++++++++++++ ....132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 35 +++++++++++++++++ easybuild/easyconfigs/i/intel/intel-2017a.eb | 24 ++++++++++++ 8 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb new file mode 100644 index 0000000000..80e701d1a6 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..4b07bc6dde --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] + +checksums = ['41a0e8850ebb5f7169076c89be743ee2'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..11f7aab8ea --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2017.1.132' +versionsuffix = '-GCC-6.3.0-2.27' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..4c71563eb3 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] + +checksums = ['612169f4b40cdded8e212bf097925e4f'] + +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb new file mode 100644 index 0000000000..c272ff0803 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +suff = '-GCC-6.3.0-2.27' +dependencies = [ + ('icc', compver, suff), + ('ifort', compver, suff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, suff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb new file mode 100644 index 0000000000..e28e5314fa --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2017a'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['7911c0f777c4cb04225bf4518088939e'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..3193d2cc9a --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2017a.eb b/easybuild/easyconfigs/i/intel/intel-2017a.eb new file mode 100644 index 0000000000..4e98f5a7f2 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2017a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +intelver = '2017.1.132' +gccver = '6.3.0' +binutilsver = '2.27' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', intelver, gccsuff), + ('ifort', intelver, gccsuff), + ('impi', intelver, '', ('iccifort', '%s%s' % (intelver, gccsuff))), + ('imkl', intelver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' -- GitLab From 8eb0ae0e9e97ac8862b4d35f5e7d7d41db8ab2e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2017 15:35:59 +0100 Subject: [PATCH 053/818] add missing patch file for MPFR 3.1.5 --- .../mpfr-3.1.5-allpatches-20161215.patch | 176 ++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161215.patch diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161215.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161215.patch new file mode 100644 index 0000000000..3b81ad49a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161215.patch @@ -0,0 +1,176 @@ +# All mpfr patches as of 2016-08-04 +# taken from their website: http://www.mpfr.org/mpfr-current/#download +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; -- GitLab From af8f79840ae070ffb98938da12dc96ff585f7201 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 4 Jan 2017 14:44:37 +0000 Subject: [PATCH 054/818] Add sanity check and clean up GSL 2.3 --- easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb index b5798d1552..2d15b5f44a 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb @@ -9,11 +9,16 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a and least-squares fitting.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} +toolchainopts = {'unroll': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] configopts = '--with-pic' +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + moduleclass = 'numlib' -- GitLab From 9f20c1c4dce1fd1ce333e6bc81cad28518e0a40c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2017 16:02:09 +0100 Subject: [PATCH 055/818] make sanity_check_paths more specific for GSL 2.3 --- easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb index 2d15b5f44a..2183152ee4 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2016b.eb @@ -17,8 +17,9 @@ source_urls = [GNU_SOURCE] configopts = '--with-pic' sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'include', 'lib', 'share'], + 'files': ['bin/gsl-config', 'lib/libgsl.a', 'lib/libgsl.%s' % SHLIB_EXT, + 'lib/libgslcblas.a', 'lib/libgslcblas.%s' % SHLIB_EXT], + 'dirs': ['include/gsl', 'lib/pkgconfig', 'share'], } moduleclass = 'numlib' -- GitLab From 1cbf4f37d847820aa8e8cf747f3ef6babb1533fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2017 16:15:53 +0100 Subject: [PATCH 056/818] bump LAPACK to 3.7.0, include required patch file for combining OpenBLAS 0.2.19 and LAPACK 3.7.0 --- easybuild/easyconfigs/f/foss/foss-2017a.eb | 2 +- ...LAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb} | 3 +- .../OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch | 35 +++++++++++++++++++ ...mpi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb} | 2 +- 4 files changed, 39 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb => OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb} (95%) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb => ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb} (95%) diff --git a/easybuild/easyconfigs/f/foss/foss-2017a.eb b/easybuild/easyconfigs/f/foss/foss-2017a.eb index 58f252b974..10b0c04f90 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017a.eb @@ -14,7 +14,7 @@ gccver = '6.3.0-2.27' blaslib = 'OpenBLAS' blasver = '0.2.19' blas = '%s-%s' % (blaslib, blasver) -blassuff = '-LAPACK-3.6.1' +blassuff = '-LAPACK-3.7.0' # toolchain used to build foss dependencies comp_mpi_tc_name = 'gompi' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index 94fc300c72..ba23eaadbf 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.19' -lapackver = '3.6.1' +lapackver = '3.7.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' @@ -35,6 +35,7 @@ source_urls = [ patches = [ (large_src, '.'), (timing_src, '.'), + 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch new file mode 100644 index 0000000000..54c1b5525d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch @@ -0,0 +1,35 @@ +fixes to combine OpenBLAS 0.2.19 with LAPACK 3.7.0 +* upstream bugfix in Makefile for LAPACK 3.7.0, cfr. https://github.com/Reference-LAPACK/lapack/commit/c5788233f95fed2c7f008ea079e8257a85348287 +* fix copying of lapacke_mangling.h, since it was renamed in LAPACK 3.7.0 +author: Kenneth Hoste (HPC-UGent) +--- OpenBLAS-0.2.19/Makefile.install.orig 2017-01-04 15:51:12.483541471 +0100 ++++ OpenBLAS-0.2.19/Makefile.install 2017-01-04 15:51:27.583647000 +0100 +@@ -50,7 +50,7 @@ + @echo Copying LAPACKE header files to $(DESTDIR)$(OPENBLAS_INCLUDE_DIR) + @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke.h" + @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_config.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_config.h" +- @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_mangling_with_flags.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_mangling.h" ++ @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_mangling.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_mangling.h" + @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_utils.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_utils.h" + endif + +--- OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt.orig ++++ OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt +@@ -454,7 +454,6 @@ set(ZLASRC + zgelqt.f zgelqt3.f zgemlqt.f + zgetsls.f zgeqr.f zlatsqr.f zlamtsqr.f zgemqr.f + zgelq.f zlaswlq.f zlamswlq.f zgemlq.f +- ztplqt.f ztplqt2.f ztpmlqt.f + zhetrd_2stage.f zhetrd_he2hb.f zhetrd_hb2st.F zhb2st_kernels.f + zheevd_2stage.f zheev_2stage.f zheevx_2stage.f zheevr_2stage.f + zhbev_2stage.f zhbevx_2stage.f zhbevd_2stage.f zhegv_2stage.f) +--- OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile.orig ++++ OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile +@@ -464,7 +464,6 @@ ZLASRC = \ + zgelqt.o zgelqt3.o zgemlqt.o \ + zgetsls.o zgeqr.o zlatsqr.o zlamtsqr.o zgemqr.o \ + zgelq.o zlaswlq.o zlamswlq.o zgemlq.o \ +- ztplqt.o ztplqt2.o ztpmlqt.o \ + zhetrd_2stage.o zhetrd_he2hb.o zhetrd_hb2st.o zhb2st_kernels.o \ + zheevd_2stage.o zheev_2stage.o zheevx_2stage.o zheevr_2stage.o \ + zhbev_2stage.o zhbevx_2stage.o zhbevd_2stage.o zhegv_2stage.o diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb similarity index 95% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb index 07590857f9..3d67fae22f 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.19' -blassuff = '-LAPACK-3.6.1' +blassuff = '-LAPACK-3.7.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -- GitLab From 63dc6bc9cb64283e804e4290ccc446fc5d611ff2 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 4 Jan 2017 19:50:37 +0100 Subject: [PATCH 057/818] ENH: add support for WPS 3.8, add known_problems fixes to WRF 3.8 --- ...mpar.eb => WPS-3.8.0-intel-2016a-dmpar.eb} | 10 +-- ...s.patch => WPS-3.8.0_known_problems.patch} | 13 +++- ...S-3.8.0_netCDF-Fortran_seperate_path.patch | 71 +++++++++++++++++++ .../w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb | 1 + .../w/WRF/WRF-3.8.0_known_problems.patch | 71 +++++++++++++++++++ 5 files changed, 160 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/w/WPS/{WPS-3.8-intel-2016a-dmpar.eb => WPS-3.8.0-intel-2016a-dmpar.eb} (81%) rename easybuild/easyconfigs/w/WPS/{WPS-3.8_fix_known_problems.patch => WPS-3.8.0_known_problems.patch} (65%) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.8.0_netCDF-Fortran_seperate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0_known_problems.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.8.0-intel-2016a-dmpar.eb similarity index 81% rename from easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb rename to easybuild/easyconfigs/w/WPS/WPS-3.8.0-intel-2016a-dmpar.eb index c426109e50..ed55b813b2 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.8-intel-2016a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8.0-intel-2016a-dmpar.eb @@ -1,5 +1,5 @@ name = 'WPS' -version = '3.8' +version = '3.8.0' homepage = 'http://www.wrf-model.org' description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is @@ -9,7 +9,7 @@ description = """WRF Preprocessing System (WPS) for WRF. The Weather Research an toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'opt': True} -sources = ['%(name)sV%(version)s.TAR.gz'] +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] source_urls = [ 'http://www2.mmm.ucar.edu/wrf/src/', 'http://www.mmm.ucar.edu/wrf/src/', @@ -20,8 +20,8 @@ checksums = ['2ab4e4ddae4e105432c18c59819a4523'] # patches for known problems as of 27 Jul 2016, see # http://www2.mmm.ucar.edu/wrf/users/wpsv3.8/known-prob-3.8.html patches = [ - 'WPS_netCDF-Fortran_seperate_path.patch', - 'WPS-%(version)s_fix_known_problems.patch', + 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_known_problems.patch', ] buildtype = "dmpar" @@ -30,7 +30,7 @@ versionsuffix = '-%s' % buildtype dependencies = [ ('WRF', version, versionsuffix), ('netCDF', '4.4.0'), - ('netCDF-Fortran', '4.4.2'), + ('netCDF-Fortran', '4.4.3'), ('zlib', '1.2.8'), ('libpng', '1.6.21'), ('JasPer', '1.900.1'), diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch b/easybuild/easyconfigs/w/WPS/WPS-3.8.0_known_problems.patch similarity index 65% rename from easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch rename to easybuild/easyconfigs/w/WPS/WPS-3.8.0_known_problems.patch index e03a2fbc76..e94fa09a3a 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.8_fix_known_problems.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8.0_known_problems.patch @@ -1,5 +1,16 @@ +# ====================================================================== +# Fix known problems in WPS3.8 source code +# (http://www2.mmm.ucar.edu/wrf/users/wpsv3.8/known-prob-3.8.html) +# ====================================================================== +# +# NCAR CISL/RDA Data Type 113.0 (posted 6/16/2016) +# ================================================ +# +# Using this type of input data causes fields to shift approximately 1 degree +# longitude toward the east (when compared to raw ECMWF grib files. + --- WPS.orig/ungrib/src/rd_grib1.F 2013-06-08 00:48:10.000000000 +0200 -+++ WPS/ungrib/src/rd_grib1.F 2016-07-26 11:02:19.021497705 +0200 ++++ WPS/ungrib/src/rd_grib1.F 2016-06-30 17:18:27.000000000 +0200 @@ -406,7 +406,7 @@ !print *,'new dx = ',map%dx endif diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8.0_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-3.8.0_netCDF-Fortran_seperate_path.patch new file mode 100644 index 0000000000..a0a5dd6390 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8.0_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,71 @@ +diff -ru WPS.orig/arch/Config.pl WPS/arch/Config.pl +--- WPS.orig/arch/Config.pl 2012-04-07 00:07:24.000000000 +0200 ++++ WPS/arch/Config.pl 2012-06-19 15:33:40.998567539 +0200 +@@ -36,6 +36,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -ru WPS.orig/configure WPS/configure +--- WPS.orig/configure 2012-04-07 00:07:19.000000000 +0200 ++++ WPS/configure 2012-06-19 15:34:35.543132843 +0200 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -151,7 +156,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach + + + #Checking cross-compiling capability for some particular environment +@@ -319,9 +324,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +Only in WPS: configure.wps +diff -ru WPS.orig/util/src/Makefile WPS/util/src/Makefile +--- WPS.orig/util/src/Makefile 2012-04-07 00:07:26.000000000 +0200 ++++ WPS/util/src/Makefile 2012-06-19 15:36:39.849421166 +0200 +@@ -40,11 +40,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb index 8afc4ff822..e63ecee8b4 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb @@ -28,6 +28,7 @@ patches = [ 'WRF_parallel_build_fix.patch', 'WRF_tests_limit-runtimes.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRF-%(version)s_known_problems.patch', ] # limit parallel build to 20 diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_known_problems.patch b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_known_problems.patch new file mode 100644 index 0000000000..4e591faa37 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_known_problems.patch @@ -0,0 +1,71 @@ +# ====================================================================== +# Fix known problems in WRF3.8 source code +# (http://www2.mmm.ucar.edu/wrf/users/wrfv3.8/known-prob-3.8.html) +# ====================================================================== +# +# Problem when using tmn_update (posted September 8, 2016) +# ======================================================== +# +# An error was introduced beginning with WRF Version 3.7 in a restart run when +# the tmn_update option is used. This error is present in WRF Versions 3.7, +# 3.7.1, 3.8 and 3.8.1. When tmn_update is activated, a moving-averaged skin +# temperature (TLAG) is used as a lower boundary condition for the land model. +# Since TLAG is left out of the restart file, any restart using the tmn_update +# option will start with 0 K as the lower boundary condition for the land model. +# This will cause the soil temperature to cool gradually, eventually affecting +# the skin and atmospheric temperature. The tmn_update option can be used for +# the following land models: SLAB, Noah, NoahMP, RUC and CLM. + +diff -Naur WRFV3.orig/Registry/Registry.EM_COMMON WRFV3/Registry/Registry.EM_COMMON +--- WRFV3.orig/Registry/Registry.EM_COMMON 2016-04-05 23:09:48.000000000 +0200 ++++ WRFV3/Registry/Registry.EM_COMMON 2017-01-04 15:25:03.000000000 +0100 +@@ -1672,7 +1672,7 @@ + state real TYR ij misc 1 - rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm) "TYR" "ANNUAL MEAN SFC TEMPERATURE" "K" + state real TYRA ij misc 1 - rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm) "TYRA" "ACCUMULATED YEARLY SFC TEMPERATURE FOR CURRENT YEAR" "K" + state real TDLY ij misc 1 - rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm) "TDLY" "ACCUMULATED DAILY SFC TEMPERATURE FOR CURRENT DAY" "K" +-state real TLAG i&j misc 1 - d=(interp_mask_field:lu_index,iswater)u=(copy_fcnm) "TLAG" "DAILY MEAN SFC TEMPERATURE OF PRIOR DAYS" "K" ++state real TLAG i&j misc 1 - rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm) "TLAG" "DAILY MEAN SFC TEMPERATURE OF PRIOR DAYS" "K" + state integer NYEAR - misc 1 - r "NYEAR" "ACCUM DAYS IN A YEAR" "" + state real NDAY - misc 1 - r "NDAY" "ACCUM TIMESTEPS IN A DAY" "" + state real XLAND ij misc 1 - i02rhd=(interp_fcnm_imask)u=(copy_fcnm) "XLAND" "LAND MASK (1 FOR LAND, 2 FOR WATER)" "" + +# Problem with Cloud Fraction (posted November 30, 2016) +# ====================================================== +# +# Beginning in V3.8, a bug was introduced to cloud fraction. This is seen by +# most radiation schemes, when a microphysics scheme is used that does not have +# cloud ice (e.g. WSM3, Kessler). When WSM3 or Kessler is used, cloud fraction +# is not computed, and hence a radiation scheme will not see any cloud. This +# results in unrealistic surface temperature and incorrect upwelling long-wave +# radiation at the top of the atmosphere. + +diff -Naur WRFV3.orig/phys/module_radiation_driver.F WRFV3/phys/module_radiation_driver.F +--- WRFV3.orig/phys/module_radiation_driver.F 2016-03-30 22:36:24.000000000 +0200 ++++ WRFV3/phys/module_radiation_driver.F 2017-01-04 15:26:17.000000000 +0100 +@@ -1120,7 +1120,7 @@ + + IF ( ICLOUD == 1 ) THEN + +- IF ( F_QC .AND. F_QI ) THEN ++ IF ( F_QC .OR. F_QI ) THEN + ! Call to cloud fraction routine based on Randall 1994 (Hong Pan 1998) + + CALL wrf_debug (1, 'CALL cldfra1') +@@ -1192,7 +1192,7 @@ + + ELSE IF ( ICLOUD == 2 ) THEN + +- IF ( F_QC .AND. F_QI ) THEN ++ IF ( F_QC .OR. F_QI ) THEN + CALL wrf_debug (1, 'CALL cldfra2') + CALL cal_cldfra2(CLDFRA,qc,qi,F_QC,F_QI, & + ids,ide, jds,jde, kds,kde, & +@@ -1205,7 +1205,7 @@ + !+---+-----------------------------------------------------------------+ + + ELSEIF (ICLOUD == 3) THEN +- IF ( F_QC .AND. F_QI ) THEN ++ IF ( F_QC .OR. F_QI ) THEN + IF ( F_QS ) THEN + DO j = jts,jte + DO k = kts,kte -- GitLab From d38f805f563026b6da2d8457fc424b5f24a3c001 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 5 Jan 2017 12:12:16 +1300 Subject: [PATCH 058/818] Add the directory to the executable PATH --- easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb index bd778d69d8..64cd6052f9 100644 --- a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] +modextrapaths = {'PATH': ''} + sanity_check_paths = { 'files': ['NetLogo', 'NetLogo3D', 'NetLogoLogging'], 'dirs': ['app', 'runtime'], -- GitLab From 5b5b3f3a0962d264ebf84d5b887ec91c28176ed0 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 5 Jan 2017 13:33:42 +1300 Subject: [PATCH 059/818] Remove extra modextrapaths as not needed --- easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb index 64cd6052f9..bd778d69d8 100644 --- a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb @@ -17,8 +17,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] -modextrapaths = {'PATH': ''} - sanity_check_paths = { 'files': ['NetLogo', 'NetLogo3D', 'NetLogoLogging'], 'dirs': ['app', 'runtime'], -- GitLab From f7a88f53624fe8ad0738c6bd8b71edee1365f8c3 Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Thu, 5 Jan 2017 06:37:58 +0100 Subject: [PATCH 060/818] [foss/2016b] Boost 1.63.0 Note: SOURCEFORGE_SOURCE returned a wrong tarball with missing files --- .../Boost-1.63.0-foss-2016b-Python-2.7.12.eb | 23 ++++++++++++++++ .../Boost-1.63.0-foss-2016b-Python-3.5.2.eb | 27 +++++++++++++++++++ .../b/Boost/Boost-1.63.0_python3.patch | 24 +++++++++++++++++ 3 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0_python3.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3f0c47295f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..7947adb6bb --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +patches = [ + 'Boost-%(version)s_python3.patch', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '3.5.2'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0_python3.patch b/easybuild/easyconfigs/b/Boost/Boost-1.63.0_python3.patch new file mode 100644 index 0000000000..279cbfb666 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0_python3.patch @@ -0,0 +1,24 @@ +#Boost checks Python include in $(prefix)/include/python$(version) +#some cases it is in $(prefix)/include/python$(version)m +#see more: https://svn.boost.org/trac/boost/ticket/11120 +# Aug 27th 2016 by B. Hajgato (Free Univeristy Brussels - VUB) +--- boost_1_60_0/tools/build/src/tools/python.jam.org 2015-10-16 20:55:36.000000000 +0200 ++++ boost_1_60_0/tools/build/src/tools/python.jam 2016-07-27 16:20:52.549560154 +0200 +@@ -539,7 +539,16 @@ + } + else + { +- includes ?= $(prefix)/include/python$(version) ; ++ if not($(prefix)/include/python$(version)m) ++ { ++ debug-message "Used include path: $(prefix)/include/python$(version)m" ; ++ includes ?= $(prefix)/include/python$(version)m ; ++ } ++ else ++ { ++ debug-message "Used include path: $(prefix)/include/python$(version)" ; ++ includes ?= $(prefix)/include/python$(version) ; ++ } + + local lib = $(exec-prefix)/lib ; + libraries ?= $(lib)/python$(version)/config $(lib) ; -- GitLab From 985ed0e13c775cd78f1ce5aba13b810f51bc55a7 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 6 Jan 2017 14:29:32 +1300 Subject: [PATCH 061/818] Reversion to older versions of packages per request from K.H. --- .../p/Python/Python-2.7.11-foss-2015a.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 60154d0a99..a55f5a9bff 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} numpyversion = '1.10.1' -scipyversion = '0.17.0' +scipyversion = '0.16.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -30,12 +30,12 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# package versions updated 1 April 2016 +# package versions updated 28 May 2015 exts_list = [ - ('setuptools', '20.3.1', { + ('setuptools', '18.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '8.1.1', { + ('pip', '7.1.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { @@ -51,7 +51,7 @@ exts_list = [ ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), - ('mpi4py', '2.0.0', { + ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { @@ -72,7 +72,7 @@ exts_list = [ ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.5.2', { + ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), @@ -80,7 +80,7 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), - ('decorator', '4.0.9', { + ('decorator', '4.0.4', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), ('arff', '2.1.0', { @@ -97,7 +97,7 @@ exts_list = [ ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), - ('pyparsing', '2.1.1', { + ('pyparsing', '2.0.6', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('netifaces', '0.10.4', { @@ -112,10 +112,10 @@ exts_list = [ ('mock', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], }), - ('pytz', '2016.3', { + ('pytz', '2015.7', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), - ('pandas', '0.18.0', { + ('pandas', '0.17.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), ('enum34', '1.1.2', { @@ -128,7 +128,7 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), - ('virtualenv', '15.0.1', { + ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), ] -- GitLab From 22daeb0d1dabbb4d87302b8e709f8e4ca418581f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 6 Jan 2017 14:48:21 +1300 Subject: [PATCH 062/818] Removal of custom site-specific commands --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 16 ++++++++++------ easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 16 ++++++++++------ 2 files changed, 20 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index c92177166e..88b4f2e32e 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -13,14 +13,18 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. sources = ['%(name)s%(version)s.tar.bz2'] -dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_80')] - -postinstallcmds = ['chmod a+x %(installdir)s/submit%(name)s'] +dependencies = [ + ('BLAST', '2.2.26', "-Linux_x86_64"), + ('Java', '1.7.0_80'), +] sanity_check_paths = { - 'files': ['submitI-TASSER', 'I-TASSERmod/runI-TASSER.pl'], - 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'] + 'files': ['I-TASSERmod/runI-TASSER.pl'], + 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'], } +# You may find it desirable to put this variable in the module file. +# The command to do so has been put here (commented out) as a convenience. +#modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } + moduleclass = 'bio' -modextravars = { 'IMINTASSERDB' : '/share/db/I-TASSER/%(version)s' } diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 93f184aa24..fccdce2d50 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -13,14 +13,18 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. sources = ['%(name)s%(version)s.tar.bz2'] -dependencies = [('BLAST', '2.2.26', "-Linux_x86_64"), ('Java', '1.7.0_80')] - -postinstallcmds = ['chmod a+x %(installdir)s/submit%(name)s'] +dependencies = [ + ('BLAST', '2.2.26', "-Linux_x86_64"), + ('Java', '1.7.0_80'), +] sanity_check_paths = { - 'files': ['submitI-TASSER', 'I-TASSERmod/runI-TASSER.pl'], - 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'] + 'files': ['I-TASSERmod/runI-TASSER.pl'], + 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'], } +# You may find it desirable to put this variable in the module file. +# The command to do so has been put here (commented out) as a convenience. +#modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } + moduleclass = 'bio' -modextravars = { 'IMINTASSERDB' : '/share/db/I-TASSER/%(version)s' } -- GitLab From c0b3371903dda1d43687af13ccd5e7eef93f7c74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Jan 2017 21:19:29 +0100 Subject: [PATCH 063/818] update FFTW easyconfig to use FFTW easyblock (cfr. https://github.com/hpcugent/easybuild-easyblocks/pull/1083) --- .../f/FFTW/FFTW-3.3.5-gompi-2017a.eb | 21 ------------------- easybuild/easyconfigs/f/foss/foss-2017a.eb | 2 +- 2 files changed, 1 insertion(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb index 6975badd80..77015a0ad7 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'FFTW' version = '3.3.5' @@ -13,23 +11,4 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -# FIXME -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2017a.eb b/easybuild/easyconfigs/f/foss/foss-2017a.eb index 10b0c04f90..badece0d08 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017a.eb @@ -28,7 +28,7 @@ dependencies = [ ('GCC', gccver), ('OpenMPI', '2.0.2', '', ('GCC', gccver)), (blaslib, blasver, blassuff, ('GCC', gccver)), - ('FFTW', '3.3.5', '', comp_mpi_tc), # FIXME: --enable-sse2 --enable-avx --enable-avx2 --enable-avx512 + ('FFTW', '3.3.5', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] -- GitLab From f27abc1a4d36d66db42a8aadbe96ccef67100ccc Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 6 Jan 2017 15:28:09 -0600 Subject: [PATCH 064/818] Changed the homepage and fixed formatting for modextrapaths --- .../c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index 2be243b7e0..5017e132ee 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -7,7 +7,7 @@ easyblock = "Tarball" name = 'ConnectomeWorkbench' version = '1.2.2' -homepage = 'http://www.humanconnectome.org/software/get-connectome-workbench.html' +homepage = 'http://www.humanconnectome.org/software/connectome-workbench.html' description = """Connectome Workbench is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, @@ -20,8 +20,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://ftp.humanconnectome.org/workbench/'] sources = ['workbench-rh_linux64-v%(version)s.zip'] -modextrapaths = {'PATH': 'bin_rh_linux64', 'LIBRARY_PATH': 'libs_rh_linux64', -'LD_LIBRARY_PATH': 'libs_rh_linux64'} +modextrapaths = { + 'PATH': 'bin_rh_linux64', + 'LIBRARY_PATH': 'libs_rh_linux64', + 'LD_LIBRARY_PATH': 'libs_rh_linux64'} sanity_check_paths = { 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", -- GitLab From 589730ef1c546c9c29aa64287ca2884dce1885ea Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 6 Jan 2017 15:44:12 -0600 Subject: [PATCH 065/818] Fixed formatting for modextrapaths --- .../c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index 5017e132ee..edd7b1aa5d 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -23,7 +23,8 @@ sources = ['workbench-rh_linux64-v%(version)s.zip'] modextrapaths = { 'PATH': 'bin_rh_linux64', 'LIBRARY_PATH': 'libs_rh_linux64', - 'LD_LIBRARY_PATH': 'libs_rh_linux64'} + 'LD_LIBRARY_PATH': 'libs_rh_linux64', +} sanity_check_paths = { 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", -- GitLab From e37eedba449408249e6ffd00970e1b007887cd2f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 10 Jan 2017 00:30:48 +0100 Subject: [PATCH 066/818] adding easyconfigs: EMBOSS-6.6.0-foss-2016b.eb, libharu-2.3.0-foss-2016b.eb --- .../e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb | 44 +++++++++++++++++++ .../l/libharu/libharu-2.3.0-foss-2016b.eb | 39 ++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb new file mode 100644 index 0000000000..ad22d09979 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -0,0 +1,44 @@ +# authors: Kenneth Hoste (Ghent University), George Tsouloupas , Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. + EMBOSS is a free Open Source software analysis package specially developed for + the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] +sources = [SOURCE_TAR_GZ] + +patches = ['EMBOSS_disable-embossupdate.patch'] + +dependencies = [ + ('libharu', '2.3.0'), + ('Java', '1.7.0_80', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb new file mode 100644 index 0000000000..2b4825fe33 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [' https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('libpng', '1.6.24')] + +builddependencies = [('CMake', '3.6.2')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' -- GitLab From 6a88204b7332e9fe6c36e0ceb47b058d637d072b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 10 Jan 2017 14:56:56 +1300 Subject: [PATCH 067/818] Updates to packages in foss 2015a easyconfig for Python, and some tweaks to foss 2016a toolchain recommended by K.H. --- .../p/Python/Python-3.5.1-foss-2015a.eb | 24 +++++++++---------- .../p/Python/Python-3.5.1-foss-2016a.eb | 10 ++++++++ 2 files changed, 22 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index d5d4531b05..f2338d2948 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -7,7 +7,7 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.10.1' +numpyversion = '1.10.4' scipyversion = '0.17.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] @@ -29,12 +29,12 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! -# package versions updated 1 April 2016 +# package versions updated 10 Jan 2017 cf. EasyConfig for Python-3.5.1-foss-2016a.eb exts_list = [ - ('setuptools', '20.3.1', { + ('setuptools', '20.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '8.1.1', { + ('pip', '8.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { @@ -64,13 +64,13 @@ exts_list = [ ('lockfile', '0.12.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.24b0', { - 'source_urls': ['http://www.cython.org/release/'], + ('Cython', '0.23.4', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.5.2', { + ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), @@ -98,7 +98,7 @@ exts_list = [ ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), - ('pyparsing', '2.1.1', { + ('pyparsing', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('netifaces', '0.10.4', { @@ -107,16 +107,16 @@ exts_list = [ ('netaddr', '0.7.18', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), - ('pytz', '2016.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.18.0', { + ('pandas', '0.17.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), ('bitstring', '3.1.3', { 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), + ('pytz', '2016.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), ('virtualenv', '15.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 129c326cbb..edc992932d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -111,6 +111,16 @@ exts_list = [ ('pandas', '0.17.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('pytz', '2016.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('virtualenv', '15.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' -- GitLab From 4403b680efeb23424afb468233d8752c218e2e0d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 10 Jan 2017 16:53:27 +1300 Subject: [PATCH 068/818] EasyConfig for the X11 bundle using the foss-2015a toolchain --- .../fontconfig-2.12.1-foss-2015a.eb | 22 +++ .../x/X11/X11-20160819-foss-2015a.eb | 131 ++++++++++++++++++ 2 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb new file mode 100644 index 0000000000..815b77935c --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), # Selected an older version for consistency + ('freetype', '2.6.2'), # Selected an older version for consistency +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb new file mode 100644 index 0000000000..89cbcbda34 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb @@ -0,0 +1,131 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20160819' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] +dependencies = [ + ('freetype', '2.6.2'), # Slightly older version than in foss-2016b for consistency + ('fontconfig', '2.12.1'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.0', { + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.3', common_specs), + ('bigreqsproto', '1.1.2', common_specs), + ('compositeproto', '0.4.2', common_specs), + ('damageproto', '1.2.1', common_specs), + ('dmxproto', '2.3.1', common_specs), + ('dri2proto', '2.8', common_specs), + ('dri3proto', '1.0', common_specs), + ('fixesproto', '5.0', common_specs), + ('fontsproto', '2.1.3', common_specs), + ('glproto', '1.4.17', common_specs), + ('inputproto', '2.3.1', common_specs), + ('kbproto', '1.0.7', common_specs), + ('presentproto', '1.0', common_specs), + ('randrproto', '1.5.0', common_specs), + ('recordproto', '1.14.2', common_specs), + ('renderproto', '0.11', common_specs), + ('resourceproto', '1.2.0', common_specs), + ('scrnsaverproto', '1.2.2', common_specs), + ('videoproto', '2.3.3', common_specs), + ('xcmiscproto', '1.2.2', common_specs), + ('xextproto', '7.3.0', common_specs), + ('xf86bigfontproto', '1.2.0', common_specs), + ('xf86dgaproto', '2.1', common_specs), + ('xf86driproto', '2.1.1', common_specs), + ('xf86vidmodeproto', '2.3.1', common_specs), + ('xineramaproto', '1.2.1', common_specs), + ('xproto', '7.0.28', common_specs), + ('libXau', '1.0.8', common_specs), + ('libXdmcp', '1.1.2', common_specs), + ('xcb-proto', '1.11', common_specs), + ('libxcb', '1.11.1', common_specs), + ('xtrans', '1.3.5', common_specs), + ('libxkbcommon', '0.6.1', { + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.3', common_specs), + ('libXext', '1.3.3', common_specs), + ('libFS', '1.0.7', common_specs), + ('libICE', '1.0.9', common_specs), + ('libSM', '1.2.2', common_specs), + ('libXScrnSaver', '1.2.2', common_specs), + ('libXt', '1.1.5', common_specs), + ('libXmu', '1.1.2', common_specs), + ('libXpm', '3.5.11', common_specs), + ('libXaw', '1.0.13', common_specs), + ('libXfixes', '5.0.2', common_specs), + ('libXcomposite', '0.4.4', common_specs), + ('libXrender', '0.9.9', common_specs), + ('libXcursor', '1.1.14', common_specs), + ('libXdamage', '1.1.4', common_specs), + ('libfontenc', '1.1.3', common_specs), + ('libXfont', '1.5.1', common_specs), + ('libXft', '2.3.2', common_specs), + ('libXi', '1.7.6', common_specs), + ('libXinerama', '1.1.3', common_specs), + ('libXrandr', '1.5.0', common_specs), + ('libXres', '1.0.7', common_specs), + ('libXtst', '1.2.2', common_specs), + ('libXv', '1.0.10', common_specs), + ('libXvMC', '1.0.9', common_specs), + ('libXxf86dga', '1.1.4', common_specs), + ('libXxf86vm', '1.1.4', common_specs), + ('libdmx', '1.1.3', common_specs), + ('libpciaccess', '0.13.4', common_specs), + ('libxkbfile', '1.0.9', common_specs), + ('libxshmfence', '1.2', common_specs), + ('xcb-util', '0.4.0', common_specs), + ('xcb-util-image', '0.4.0', common_specs), + ('xcb-util-keysyms', '0.4.0', common_specs), + ('xcb-util-renderutil', '0.3.9', common_specs), + ('xcb-util-wm', '0.4.1', common_specs), + ('xcb-util-cursor', '0.1.3', common_specs), +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 980e36ac973fdd7815f389a3c3b78821f5299ab7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2017 10:09:09 +0100 Subject: [PATCH 069/818] adding easyconfigs: rhdf5-2.18.0-intel-2016b-R-3.3.1.eb --- .../rhdf5/rhdf5-2.18.0-intel-2016b-R-3.3.1.eb | 29 +++++++++++++++++++ .../zlibbioc-1.20.0-intel-2016b-R-3.3.1.eb | 26 +++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/rhdf5/rhdf5-2.18.0-intel-2016b-R-3.3.1.eb create mode 100644 easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.20.0-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/r/rhdf5/rhdf5-2.18.0-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/r/rhdf5/rhdf5-2.18.0-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..4948bcb9cc --- /dev/null +++ b/easybuild/easyconfigs/r/rhdf5/rhdf5-2.18.0-intel-2016b-R-3.3.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rhdf5' +version = '2.18.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/rhdf5.html' +description = "This R/Bioconductor package provides an interface between HDF5 and R." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://bioconductor.org/packages/release/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.3/bioc/src/contrib/', +] +sources = ['rhdf5_%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.3.1'), + ('zlibbioc', '1.20.0', versionsuffix), + ('HDF5', '1.8.17'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.20.0-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.20.0-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..4bfc5357a0 --- /dev/null +++ b/easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.20.0-intel-2016b-R-3.3.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'zlibbioc' +version = '1.20.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/zlibbioc.html' +description = """This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have + these available via other means.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://bioconductor.org/packages/release/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.3/bioc/src/contrib/', +] +sources = ['zlibbioc_%(version)s.tar.gz'] + +dependencies = [('R', '3.3.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' -- GitLab From fd5e19bec1c8ba90898cc8fad6f5b417d458ee8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2017 10:27:21 +0100 Subject: [PATCH 070/818] adding easyconfigs: ack-2.14.eb --- easybuild/easyconfigs/a/ack/ack-2.14.eb | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/ack/ack-2.14.eb diff --git a/easybuild/easyconfigs/a/ack/ack-2.14.eb b/easybuild/easyconfigs/a/ack/ack-2.14.eb new file mode 100644 index 0000000000..7f10d7a34e --- /dev/null +++ b/easybuild/easyconfigs/a/ack/ack-2.14.eb @@ -0,0 +1,24 @@ +easyblock = 'CmdCp' + +name = 'ack' +version = '2.14' + +homepage = 'http://beyondgrep.com/' +description = "ack is a tool like grep, optimized for programmers" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [homepage] +# use 'cp' as 'unpack' command +sources = [('ack-%(version)s-single-file', "cp %s ack")] + +cmds_map = [('ack', "chmod a+rx ack")] + +files_to_copy = [(['ack'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ack'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 951d0444b47077363870f8e3baeb30130f193c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2017 10:56:07 +0100 Subject: [PATCH 071/818] enable running of tests in FFTW easyconfig using gompi/2017a --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb index 77015a0ad7..66f9239e19 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb @@ -11,4 +11,6 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] +runtest = 'check' + moduleclass = 'numlib' -- GitLab From 044778cbccb3c49d0b131b331cc00f4ac7381e73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2017 11:01:45 +0100 Subject: [PATCH 072/818] sync Python easyconfigs with foss/2015a with equivalent ones in develop --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 5 +++-- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index a55f5a9bff..c5fe86070e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -23,14 +23,14 @@ dependencies = [ ('SQLite', '3.10.0'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # required for pycrypto -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# package versions updated 28 May 2015 +# package versions updated May 28th 2015 exts_list = [ ('setuptools', '18.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index f2338d2948..68a366030d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -20,8 +20,9 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.10.0'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -29,7 +30,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! -# package versions updated 10 Jan 2017 cf. EasyConfig for Python-3.5.1-foss-2016a.eb +# package versions updated Feb 25th 2016 exts_list = [ ('setuptools', '20.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], -- GitLab From b612216bacefe6526966216851e58965ebec7139 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2017 15:05:32 +0100 Subject: [PATCH 073/818] update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests --- .../f/FFTW/FFTW-3.3.5-gompi-2016.07.eb | 20 +----------------- .../f/FFTW/FFTW-3.3.5-gompi-2016.09.eb | 20 +----------------- .../f/FFTW/FFTW-3.3.5-gompi-2016b.eb | 20 +----------------- .../f/FFTW/FFTW-3.3.5-gompic-2016.10.eb | 20 +----------------- .../f/FFTW/FFTW-3.3.5-intel-2016b.eb | 21 +++++-------------- 5 files changed, 9 insertions(+), 92 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb index 854d665922..b4418131e1 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'FFTW' version = '3.3.5' @@ -13,22 +11,6 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} +runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb index 95601b61f5..2b26aebdb1 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'FFTW' version = '3.3.5' @@ -13,22 +11,6 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} +runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb index e222c97b5d..2398a80c24 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'FFTW' version = '3.3.5' @@ -13,22 +11,6 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} +runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.eb index 2499d7f87a..802e40e5f2 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'FFTW' version = '3.3.5' @@ -13,22 +11,6 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-avx --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-avx --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} +runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb index 6fcdd25eb5..aba6939866 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'FFTW' version = '3.3.5' @@ -13,22 +11,13 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -common_configopts = "--enable-threads --enable-openmp --with-pic" - # no quad precision, requires GCC v4.6 or higher # see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma +use_fma = False -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], - 'dirs': ['lib/pkgconfig'], -} +runtest = 'check' moduleclass = 'numlib' -- GitLab From f2eba976b9a31b86c26cac9f3b7b2584d5477356 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Tue, 10 Jan 2017 16:40:56 +0200 Subject: [PATCH 074/818] Remove redudant byacc in libmatheval and remove trivial GSL update --- easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb | 4 ++-- .../l/libmatheval/libmatheval-1.1.11-foss-2016b.eb | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb index c5ee5164d4..f7799c2690 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb @@ -11,9 +11,9 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'version': '2016b', 'name': 'foss'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] -configopts = "--with-pic" +configopts = '--with-pic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb index 187e735268..ae6c12b340 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb @@ -16,7 +16,6 @@ source_urls = [GNU_SOURCE] dependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('byacc', '20160606'), ('Guile', '1.8.8'), ] -- GitLab From a6f8634b21cff39fe345e13342495b947211a9a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2017 20:23:49 +0100 Subject: [PATCH 075/818] bump to libxsmm 1.6.4 --- easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb | 2 +- ...{libxsmm-1.6-intel-2016b.eb => libxsmm-1.6.4-intel-2016b.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libxsmm/{libxsmm-1.6-intel-2016b.eb => libxsmm-1.6.4-intel-2016b.eb} (97%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb index cd0f3a9a66..0ca8d21ab0 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('Libint', '1.1.6'), ('libxc', '2.2.3'), ('PLUMED', '2.2.3'), - ('libxsmm', '1.6'), + ('libxsmm', '1.6.4'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-intel-2016b.eb similarity index 97% rename from easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb rename to easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-intel-2016b.eb index bb0cffc7fe..8418328180 100644 --- a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-intel-2016b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libxsmm' -version = '1.6' +version = '1.6.4' homepage = 'https://github.com/hfp/libxsmm' description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications -- GitLab From a8bbc9ddafb2c073711bf7a5ff3296b4a5acb4fe Mon Sep 17 00:00:00 2001 From: Javier Antonio Ruiz Bosch Date: Tue, 10 Jan 2017 16:26:22 -0500 Subject: [PATCH 076/818] New easyconfig file for Yade-2016.06a with foss-2016b toolchain --- .../Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bd962a1366 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '2016.06a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': foss'version': '2016b'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Yade-%(version)s_include-signal.patch'] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('CGAL', '4.8.1', versionsuffix), + ('GDB', '7.11.1', versionsuffix), + ('GL2PS', '1.3.9'), + ('GTS', '0.7.6'), + ('IPython', '5.1.0', versionsuffix), + ('libQGLViewer', '2.6.3'), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.3', versionsuffix), + ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.12'), + ('Qt5', '5.7.0'), + ('SQLite', '3.13.0'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('CMake', '3.7.1'), + ('Eigen', '3.2.9'), +] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' % SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From 1c0dbbadb2418d1d81de6e33d89942896cbd31ba Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 11 Jan 2017 11:27:01 +1300 Subject: [PATCH 077/818] Add pkg-config easyconfig (needed dependency) --- .../pkg-config-0.29.1-foss-2015a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2015a.eb new file mode 100644 index 0000000000..ab1875711a --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c8e921cbc2ef59a291e511c11167edaef68bd2ca Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 11 Jan 2017 11:27:58 +1300 Subject: [PATCH 078/818] Remove some unnecessary comments --- .../easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb index 815b77935c..dc6e546916 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2015a.eb @@ -13,8 +13,8 @@ source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('expat', '2.1.0'), # Selected an older version for consistency - ('freetype', '2.6.2'), # Selected an older version for consistency + ('expat', '2.1.0'), + ('freetype', '2.6.2'), ] configopts = '--disable-docs ' -- GitLab From 4e477a5d8a3da2511e186a3792fa24fcc7db958f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 11 Jan 2017 14:47:32 +1300 Subject: [PATCH 079/818] Removed an unnecessary comment --- easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb index 89cbcbda34..ca30f6a696 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb @@ -21,7 +21,7 @@ builddependencies = [ ('pkg-config', '0.29.1'), ] dependencies = [ - ('freetype', '2.6.2'), # Slightly older version than in foss-2016b for consistency + ('freetype', '2.6.2'), ('fontconfig', '2.12.1'), ('zlib', '1.2.8'), ('bzip2', '1.0.6'), -- GitLab From bb1bceb47f8e8874d26df31de22b873c334498ed Mon Sep 17 00:00:00 2001 From: Javier Antonio Ruiz Bosch Date: Wed, 11 Jan 2017 00:16:06 -0500 Subject: [PATCH 080/818] missing dependencies --- .../CGAL-4.8.1-foss-2016b-Python-2.7.12.eb | 36 ++++ .../c/CMake/CMake-3.7.1-foss-2016b.eb | 31 ++++ .../e/Eigen/Eigen-3.2.9-foss-2016b.eb | 13 ++ .../f/freeglut/freeglut-3.0.0-foss-2016b.eb | 35 ++++ .../GDB-7.11.1-foss-2016b-Python-2.7.12.eb | 35 ++++ .../g/GL2PS/GL2PS-1.3.9-foss-2016b.eb | 32 ++++ .../easyconfigs/g/GTS/GTS-0.7.6-foss-2016b.eb | 25 +++ .../IPython-5.1.0-foss-2016b-Python-2.7.12.eb | 155 ++++++++++++++++++ .../l/Loki/Loki-0.1.7-foss-2016b.eb | 24 +++ .../libQGLViewer-2.6.3-foss-2016b.eb | 20 +++ .../m/MPFR/MPFR-3.1.4-foss-2016b.eb | 26 +++ ...inieigen-0.5.3-foss-2016b-Python-2.7.12.eb | 26 +++ .../PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb | 30 ++++ .../path.py-8.2.1-foss-2016b-Python-2.7.12.eb | 33 ++++ .../pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb | 19 +++ ...-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb | 33 ++++ .../easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 33 ++++ .../testpath-0.3-foss-2016b-Python-2.7.12.eb | 30 ++++ .../VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb | 58 +++++++ .../wcwidth-0.1.7-foss-2016b-Python-2.7.12.eb | 30 ++++ .../Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 124 +++++++------- 21 files changed, 786 insertions(+), 62 deletions(-) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..e32190898d --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Boost', '1.61.0', versionsuffix), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), +] + +builddependencies = [ + ('CMake', '3.7.1'), + ('Eigen', '3.2.9'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb new file mode 100644 index 0000000000..e459f784ef --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb new file mode 100644 index 0000000000..ce9863f2a8 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.9' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016b.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016b.eb new file mode 100644 index 0000000000..9a0faa6f49 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.7.1')] + +dependencies = [ + ('X11', '20160819'), + ('libGLU', '9.0.0'), + ('Mesa', '12.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f10761fccd --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.2.0'), + ('Python', '2.7.12'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb new file mode 100644 index 0000000000..153b5aa920 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.7.1'), +] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.26'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016b.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016b.eb new file mode 100644 index 0000000000..a04d059816 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.49.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..df95bd6282 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,155 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +dependencies = [ + ('Python', '2.7.12'), + ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), + # required by 'nbconvert', but causes problems w.r.t. 'backports' module... + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('entrypoints', '0.2.2', versionsuffix), + ('path.py', '8.2.1', versionsuffix), + ('prompt-toolkit', '1.0.6', versionsuffix), +] + +# this is a bundle of Python packages +# XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have +# to be included as dependencies because bundling wheels does not work +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2016.8.8', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools', '25.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + # disabled because entrypoints on which this depends pull in configparser, which causes problems + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('nbconvert', '4.2.0', { + # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + #}), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], + 'modulename': 'IPython', + }), + ('ipywidgets', '5.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '1.2.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb new file mode 100644 index 0000000000..63a5c28598 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016b.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016b.eb new file mode 100644 index 0000000000..faac098188 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016b.eb @@ -0,0 +1,20 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libGLU', '9.0.0'), +] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb new file mode 100644 index 0000000000..d9a98da483 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.1')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..b281fdb609 --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('Eigen', '3.2.9'), + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..372e050018 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('GLib', '2.49.5'), + ('GTS' ,'0.7.6'), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..85d32100c5 --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'path.py' +version = '8.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaraco/path.py' +description = """path.py is a Python library implementing path objects as first-class entities, + allowing common operations on files to be invoked on those path objects directly.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/fc/fc/dcae2146aed6becbea77158eddb4e437718170efeade0f7fdf0aebe46b94/'] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..77fa36d059 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..e6261f564a --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/eb/81/a7ad3c223f323d05381208c262889bd09577852bd5044a13965a9a13f5ed/'] +sources = ['prompt_toolkit-%(version)s-py2-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('wcwidth', '0.1.7', versionsuffix), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb new file mode 100644 index 0000000000..9d87351ad2 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.26'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0c3651f6d7 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3054f25a62 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,58 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '7.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.6.1')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', 'mkg3states']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..277bc0108a --- /dev/null +++ b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'wcwidth' +version = '0.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jquast/wcwidth' +description = """wcwidth is a low-level Python library to simplify Terminal emulation.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/'] +sources = ['%(name)s-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/wcwidth'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index bd962a1366..e778315048 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -1,62 +1,62 @@ -easyblock = 'CMakeMake' - -name = 'Yade' -version = '2016.06a' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://yade-dem.org/doc/' -description = """ Yade is an extensible open-source framework for discrete numerical models, - focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, - allowing independent implementation of new alogrithms and interfaces. - Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ - -toolchain = {'name': foss'version': '2016b'} - -source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['Yade-%(version)s_include-signal.patch'] - -dependencies = [ - ('Boost', '1.61.0', versionsuffix), - ('CGAL', '4.8.1', versionsuffix), - ('GDB', '7.11.1', versionsuffix), - ('GL2PS', '1.3.9'), - ('GTS', '0.7.6'), - ('IPython', '5.1.0', versionsuffix), - ('libQGLViewer', '2.6.3'), - ('Loki', '0.1.7'), - ('matplotlib', '1.5.3', versionsuffix), - ('minieigen', '0.5.3', versionsuffix), - ('PyGTS', '0.3.1', versionsuffix), - ('Python', '2.7.12'), - ('Qt5', '5.7.0'), - ('SQLite', '3.13.0'), - ('VTK', '6.3.0', versionsuffix), - ('zlib', '1.2.8'), -] - -builddependencies = [ - ('CMake', '3.7.1'), - ('Eigen', '3.2.9'), -] - -separate_build_dir = True - -configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' -configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' -configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' - -modextrapaths = { - 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], - 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], - 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], -} - -sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', - ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, - 'lib64/yade-%%(version)s/libyade.%s' % SHLIB_EXT)], - 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], -} - -moduleclass = 'devel' +easyblock = 'CMakeMake' + +name = 'Yade' +version = '2016.06a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Yade-%(version)s_include-signal.patch'] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('CGAL', '4.8.1', versionsuffix), + ('GDB', '7.11.1', versionsuffix), + ('GL2PS', '1.3.9'), + ('GTS', '0.7.6'), + ('IPython', '5.1.0', versionsuffix), + ('libQGLViewer', '2.6.3'), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.3', versionsuffix), + ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.12'), + ('Qt5', '5.7.0'), + ('SQLite', '3.13.0'), + ('VTK', '7.0.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('CMake', '3.7.1'), + ('Eigen', '3.2.9'), +] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' % SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From 73ee23da5cdd17ffcb8d8a7a23b18d376ec8716d Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 11 Jan 2017 09:29:17 +0100 Subject: [PATCH 081/818] Update CP2K-4.1-foss-2016b-psmp.eb Let people turn off tests that require mpi tests themselves --- easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb index 85ce41dbb8..1cc39ce082 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb @@ -30,8 +30,6 @@ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), ] -# Don't run tests, they use mpirun -runtest = False # don't use parallel make, results in compilation failure # because Fortran module files aren't created before they are needed -- GitLab From 59e9ec60a3bc7ef17e0870c2856b8957e6a9cc50 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 11 Jan 2017 09:30:46 +0100 Subject: [PATCH 082/818] Update CP2K-4.1-foss-2016b-psmp.eb Remove plumed setting, this is figured out by the easyblock. Remove the datadir copy, this is now handled by the easyblock. --- easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb index 1cc39ce082..3d337a4c78 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb @@ -40,13 +40,4 @@ type = 'psmp' # regression test reports failures ignore_regtest_fails = True -plumed = True - -postinstallcmds = [ "cp -a %(builddir)s/%(namelower)s-%(version)s/data %(installdir)s" ] - -modextravars = { - 'CP2K_DATA_DIR': '%(installdir)s/data', -} - - moduleclass = 'chem' -- GitLab From 0ba514938abccb074e6f0c2f9a32e27ddef98ef7 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 11 Jan 2017 10:38:00 +0200 Subject: [PATCH 083/818] adding easyconfigs: libmatheval-1.1.11-foss-2015b.eb, libmatheval-1.1.11-intel-2015b.eb, libmatheval-1.1.11-intel-2016a.eb, libmatheval-1.1.11-intel-2016b.eb, libmatheval-1.1.8-goolf-1.4.10.eb, libmatheval-1.1.8-ictce-5.3.0.eb --- .../easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb | 1 - .../easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb | 1 - .../easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb | 1 - .../easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb | 1 - .../easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb | 1 - .../easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb | 1 - 6 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb index e1b1e8de36..87e0b67487 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb @@ -16,7 +16,6 @@ source_urls = [GNU_SOURCE] dependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - ('byacc', '20150711'), ('Guile', '1.8.8'), ] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb index 61dae0d3d6..d95e44d0d5 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb @@ -16,7 +16,6 @@ source_urls = [GNU_SOURCE] dependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - ('byacc', '20150711'), ('Guile', '1.8.8'), ] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb index e8c49e497e..5cd1c4de66 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb @@ -16,7 +16,6 @@ source_urls = [GNU_SOURCE] dependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('byacc', '20160324'), ('Guile', '1.8.8'), ] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb index 1e97665ea8..f3389388ae 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb @@ -16,7 +16,6 @@ source_urls = [GNU_SOURCE] dependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('byacc', '20160606'), ('Guile', '1.8.8'), ] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb index 5c4d14cc82..30524efa14 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb @@ -16,7 +16,6 @@ toolchainopts = {'pic': True} dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), - ('byacc', '20120526'), ('Guile', '1.8.8'), ] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index 69e1e6bced..5b8915269a 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -16,7 +16,6 @@ toolchainopts = {'pic': True} dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), - ('byacc', '20120526'), ('Guile', '1.8.8'), ] -- GitLab From ae3203d68d2c61fe284f74f96ce50bd18aad61ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2017 10:09:36 +0100 Subject: [PATCH 084/818] adding easyconfigs: PLUMED-2.3.0-intel-2016b.eb, GSL-2.3-intel-2016b.eb --- .../easyconfigs/g/GSL/GSL-2.3-intel-2016b.eb | 19 +++++++++ .../p/PLUMED/PLUMED-2.3.0-intel-2016b.eb | 42 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2016b.eb new file mode 100644 index 0000000000..40738004ba --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb new file mode 100644 index 0000000000..a7c0ddf0f6 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.3'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 21eadc4e0cd8674d535c54587e47accadae816bd Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 11 Jan 2017 11:21:05 +0200 Subject: [PATCH 085/818] Update dependencies --- .../c/CP2K/CP2K-4.1-foss-2016b-psmp.eb | 4 +- .../l/libxsmm/libxsmm-1.6.4-foss-2016b.eb | 26 ++++++++++++ .../p/PLUMED/PLUMED-2.3.0-foss-2016b.eb | 42 +++++++++++++++++++ 3 files changed, 70 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb index 3d337a4c78..f8e72d71f0 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb @@ -22,8 +22,8 @@ patches = [ dependencies = [ ('Libint', '1.1.6'), ('libxc', '2.2.3'), - ('PLUMED', '2.2.3'), - ('libxsmm', '1.4.4'), + ('PLUMED', '2.3.0'), + ('libxsmm', '1.6.4'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-foss-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-foss-2016b.eb new file mode 100644 index 0000000000..5436a17dc9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.6.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb new file mode 100644 index 0000000000..a6e04e3481 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 4a1c656498863c1b46595db3a79849c4dafeb431 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2017 10:35:19 +0100 Subject: [PATCH 086/818] adding easyconfigs: mahotas-1.4.3-intel-2016b-Python-2.7.12.eb --- ...mahotas-1.4.3-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..dd39e28312 --- /dev/null +++ b/easybuild/easyconfigs/m/mahotas/mahotas-1.4.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'mahotas' +version = '1.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mahotas.readthedocs.io/' +description = "Mahotas is a computer vision and image processing library for Python" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' -- GitLab From 06c0ce3e0f6d44a4e7447d371d4264835f8c9a1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2017 12:52:07 +0100 Subject: [PATCH 087/818] adding easyconfigs: hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb --- ...hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..8ca6c83d64 --- /dev/null +++ b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'hyperspy' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), # provides dateutil, numpy, requests, scipy + ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.18'), + ('IPython', '5.1.0', versionsuffix), # required for ipyparallel + ('matplotlib', '1.5.3', versionsuffix), +] + +exts_list = [ + ('dill', '0.2.5', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dill'], + 'source_tmpl': 'dill-%(version)s.tgz', + }), + ('ipyparallel', '5.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipyparallel'], + }), + ('natsort', '5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/natsort'], + }), + ('requests', '2.12.4', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], + }), + ('mpmath', '0.19', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], + }), + ('sympy', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sympy'], + }), + ('tqdm', '4.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm'], + }), + ('traits', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traits'], + }), + ('pyface', '5.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyface/'], + }), + ('traitsui', '5.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitsui'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hyperspy'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From 9795462bf9146417962836bf17db58e2b59317ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 11 Jan 2017 13:18:10 +0100 Subject: [PATCH 088/818] added easyconfig for PEAR 0.9.8 starting from this version there is no -src suffix for the source files --- .../p/PEAR/PEAR-0.9.8-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb new file mode 100644 index 0000000000..87f2bda1df --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.8' + +homepage = 'http://sco.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d39df7fde8fa4786fbb4dd986811b850cc5e1784 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 11 Jan 2017 13:54:09 +0100 Subject: [PATCH 089/818] added md5 checksum --- easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb index 87f2bda1df..63d0944c28 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['1ab079a2cea61aee816012966b7ccacd'] + dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), -- GitLab From b921cea7a573e94801c912161599361abf5e58df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2017 15:48:12 +0100 Subject: [PATCH 090/818] bump PLUMED to 2.3.0 --- easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb index 0ca8d21ab0..1d55051d0c 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-intel-2016b.eb @@ -20,7 +20,7 @@ patches = [ dependencies = [ ('Libint', '1.1.6'), ('libxc', '2.2.3'), - ('PLUMED', '2.2.3'), + ('PLUMED', '2.3.0'), ('libxsmm', '1.6.4'), ] -- GitLab From 6e72b8af1ceb125be61df23b2611847a2f553064 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2017 18:48:19 +0100 Subject: [PATCH 091/818] adding easyconfigs: GroIMP-1.5.eb --- easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb | 29 ++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb diff --git a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb new file mode 100644 index 0000000000..3b5abf3832 --- /dev/null +++ b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'GroIMP' +version = '1.5' + +homepage = 'http://www.grogra.de/software/groimp' +description = "GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling platform." + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['GroIMP-%(version)s-src.zip'] + +dependencies = [ + ('Java', '1.8.0_112', '', True), +] + +builddependencies = [('ant', '1.10.0', '-Java-%(javaver)s', True)] + +install_cmd = 'cd %(name)s-%(version)s/Build && ant && cp -a ../app/* %(installdir)s/' + +sanity_check_paths = { + 'files': ['core.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use GroIMP: java -jar \\$EBROOTGROIMP/core.jar\n" + +moduleclass = 'vis' -- GitLab From a3d868e7ad26fddce79116ad0512c7cae5fb2623 Mon Sep 17 00:00:00 2001 From: Javier Antonio Ruiz Bosch Date: Wed, 11 Jan 2017 15:30:52 -0500 Subject: [PATCH 092/818] Use VTK 6.3.0 and remove patch line for intel toolchain at Qt5 easyconfig with foss toolchain and include bzip2 as dependency in yade easyconfig --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 2 -- ...thon-2.7.12.eb => VTK-6.3.0-foss-2016b-Python-2.7.12.eb} | 6 ++++-- .../y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/v/VTK/{VTK-7.0.0-foss-2016b-Python-2.7.12.eb => VTK-6.3.0-foss-2016b-Python-2.7.12.eb} (93%) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb index 9d87351ad2..91f50c61d8 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -14,8 +14,6 @@ source_urls = [ ] sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] -patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] - builddependencies = [ ('pkg-config', '0.29.1'), ] diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb similarity index 93% rename from easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb index 3054f25a62..71edba0d68 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-7.0.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ easyblock = 'CMakeMake' name = 'VTK' -version = '7.0.0' +version = '6.3.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.vtk.org' @@ -36,6 +36,7 @@ builddependencies = [('CMake', '3.6.1')] dependencies = [ ('Python', '2.7.12'), ('libGLU', '9.0.0'), + ('X11', '20160819'), ] configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT @@ -49,7 +50,8 @@ preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/sit modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { - 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', 'mkg3states']], + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], } diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index e778315048..4be110c095 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -31,7 +31,7 @@ dependencies = [ ('Python', '2.7.12'), ('Qt5', '5.7.0'), ('SQLite', '3.13.0'), - ('VTK', '7.0.0', versionsuffix), + ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), ] -- GitLab From bb2346a96ea6515fa57c0b3892de694e8addb848 Mon Sep 17 00:00:00 2001 From: Javier Antonio Ruiz Bosch Date: Wed, 11 Jan 2017 16:33:56 -0500 Subject: [PATCH 093/818] Resolving dependency conflicts and include bzip2 as Yade dependency --- .../easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 2 +- .../y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 3 ++- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb index e32190898d..9bee4db9aa 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.7.1'), + ('CMake', '3.6.1'), ('Eigen', '3.2.9'), ] diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb index 153b5aa920..2841749201 100644 --- a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), ('freeglut', '3.0.0'), - ('libpng', '1.6.26'), + ('libpng', '1.6.24'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb index 91f50c61d8..aed1d16c64 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -23,7 +23,7 @@ configopts = '-skip qtgamepad' dependencies = [ ('GLib', '2.49.5'), - ('libpng', '1.6.26'), + ('libpng', '1.6.24'), ('X11', '20160819'), ('libGLU', '9.0.0'), ] diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index 4be110c095..edce22b9ab 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -18,6 +18,7 @@ patches = ['Yade-%(version)s_include-signal.patch'] dependencies = [ ('Boost', '1.61.0', versionsuffix), + ('bzip2', '1.0.6'), ('CGAL', '4.8.1', versionsuffix), ('GDB', '7.11.1', versionsuffix), ('GL2PS', '1.3.9'), @@ -36,7 +37,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.7.1'), + ('CMake', '3.6.1'), ('Eigen', '3.2.9'), ] -- GitLab From f5694ad450d1b9907b96a558f8411f35c4fe083e Mon Sep 17 00:00:00 2001 From: Javier Antonio Ruiz Bosch Date: Wed, 11 Jan 2017 17:11:38 -0500 Subject: [PATCH 094/818] resolving dependency conflicts --- ...tplotlib-1.5.2-foss-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ .../Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..83276fb208 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index edce22b9ab..541a3b67c8 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -26,7 +26,7 @@ dependencies = [ ('IPython', '5.1.0', versionsuffix), ('libQGLViewer', '2.6.3'), ('Loki', '0.1.7'), - ('matplotlib', '1.5.3', versionsuffix), + ('matplotlib', '1.5.2', versionsuffix), ('minieigen', '0.5.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.12'), -- GitLab From ee4039f7d271eb3e96fde428acdda83ed0005bec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 08:52:55 +0100 Subject: [PATCH 095/818] fix homepage & description --- .../hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb index 8ca6c83d64..ba4de3d906 100644 --- a/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb @@ -4,11 +4,10 @@ name = 'hyperspy' version = '1.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" +homepage = 'http://hyperspy.org/' +description = """HyperSpy is an open source Python library which provides tools to facilitate the interactive + data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal + (e.g. a 2D array of spectra a.k.a spectrum image)""" toolchain = {'name': 'intel', 'version': '2016b'} -- GitLab From a10f803a7565b0b81ed6a64bfbe33cc43386f4a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 12 Jan 2017 09:17:48 +0100 Subject: [PATCH 096/818] added CD-HIT 4.6.6 changed source_url to archive subdirectory files there have no versionsuffix which prevents the use of --try-software-version --- .../c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb new file mode 100644 index 0000000000..741d95b545 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'MakeCp' + +name = "CD-HIT" +version = "4.6.6" + +homepage = 'http://weizhong-lab.ucsd.edu/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/archive/'] +sources = ['V%(version)s.tar.gz'] + +checksums = ['14f61c56b48a81edc8f1b6d9e012fe55'] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From b44d9f7bebbe03946ab434625c91e874a2d1f846 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 10:19:39 +0100 Subject: [PATCH 097/818] adding easyconfigs: matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb --- ...plotlib-1.4.3-intel-2016b-Python-2.7.12.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..94bb889523 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.7'), + ('libpng', '1.6.26'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': [('matplotlib-1.4.3_Qhull-intel-fix.patch')], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 542c17346b7541ec1550dd4b48f5ec1da3138c23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 12:19:14 +0100 Subject: [PATCH 098/818] add missing deps for GroIMP --- .../a/ant/ant-1.10.0-Java-1.8.0_112.eb | 25 +++++++++++++++++++ .../j/JUnit/JUnit-4.12-Java-1.8.0_112.eb | 22 ++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb new file mode 100644 index 0000000000..cf1f192a70 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -0,0 +1,25 @@ +name = 'ant' +version = '1.10.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_112')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb new file mode 100644 index 0000000000..363163f77e --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_112')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 71d7243f8782554dfd9f7bc94bbc067e4040422a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 12:31:08 +0100 Subject: [PATCH 099/818] adding easyconfigs: ELPA-2016.05.004-intel-2016b.eb --- .../e/ELPA/ELPA-2016.05.004-intel-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb new file mode 100644 index 0000000000..ffcf5b339a --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2016.05.004' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = ['elpa-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +buildopts = ' V=1 LIBS="$LIBSCALAPACK"' + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libelpa.a'], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' -- GitLab From fef46171e0469a4939e761d6a829e49b9f629dbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 14:22:37 +0100 Subject: [PATCH 100/818] adding easyconfigs: netCDF-4.4.1.1-intel-2016b.eb --- .../n/netCDF/netCDF-4.4.1.1-intel-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb new file mode 100644 index 0000000000..24dee36e77 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.8.18'), + ('cURL', '7.49.1'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 0ad2664ece8f1fd2f3aeeeec763c0378fefa67e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 14:41:59 +0100 Subject: [PATCH 101/818] {devel}[intel/2016b] Qt5 v5.7.1 --- .../q/Qt5/Qt5-5.7.1-intel-2016b.eb | 33 +++++++++++++++++++ .../q/Qt5/Qt5-5.7.1_fix-nan-inf.patch | 20 +++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1-intel-2016b.eb new file mode 100644 index 0000000000..1fd587b6e3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.1' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['Qt5-%(version)s_fix-nan-inf.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch new file mode 100644 index 0000000000..b9dfca8149 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch @@ -0,0 +1,20 @@ +fix compilation issue with Intel compilers: "error: more than one instance of overloaded function 'isnan'i matches the argument list" +author: Kenneth Hoste (HPC-UGent) +--- ./qtbase/src/corelib/global/qnumeric_p.h.orig 2017-01-12 14:07:25.154941190 +0100 ++++ ./qtbase/src/corelib/global/qnumeric_p.h 2017-01-12 14:08:03.841376056 +0100 +@@ -72,11 +72,11 @@ + QT_BEGIN_NAMESPACE + namespace qnumeric_std_wrapper { + // the 'using namespace std' below is cases where the stdlib already put the math.h functions in the std namespace and undefined the macros. +-static inline bool math_h_isnan(double d) { using namespace std; return isnan(d); } +-static inline bool math_h_isinf(double d) { using namespace std; return isinf(d); } ++static inline bool math_h_isnan(double d) { using namespace std; return std::isnan(d); } ++static inline bool math_h_isinf(double d) { using namespace std; return std::isinf(d); } + static inline bool math_h_isfinite(double d) { using namespace std; return isfinite(d); } +-static inline bool math_h_isnan(float f) { using namespace std; return isnan(f); } +-static inline bool math_h_isinf(float f) { using namespace std; return isinf(f); } ++static inline bool math_h_isnan(float f) { using namespace std; return std::isnan(f); } ++static inline bool math_h_isinf(float f) { using namespace std; return std::isinf(f); } + static inline bool math_h_isfinite(float f) { using namespace std; return isfinite(f); } + } + QT_END_NAMESPACE -- GitLab From 2367da192637b4ea2e9afe75f596b8d4494af0a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 15:06:48 +0100 Subject: [PATCH 102/818] adding easyconfigs: libspatialite-4.3.0a-intel-2016b.eb, GEOS-3.6.1-intel-2016b-Python-2.7.12.eb --- .../f/FreeXL/FreeXL-1.0.2-intel-2016b.eb | 22 +++++++++++++ .../GEOS-3.6.1-intel-2016b-Python-2.7.12.eb | 28 ++++++++++++++++ .../libspatialite-4.3.0a-intel-2016b.eb | 32 +++++++++++++++++++ .../p/PROJ/PROJ-4.9.3-intel-2016b.eb | 30 +++++++++++++++++ .../SWIG-3.0.11-intel-2016b-Python-2.7.12.eb | 20 ++++++++++++ 5 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb new file mode 100644 index 0000000000..7b11ad3065 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.2' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.7.1')] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9997517749 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.12')] + +builddependencies = [('SWIG', '3.0.11', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-intel-2016b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-intel-2016b.eb new file mode 100644 index 0000000000..69d644216e --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.6.1', '-Python-2.7.12'), + ('SQLite', '3.13.0'), + ('PROJ', '4.9.3'), +] + +builddependencies = [('CMake', '3.7.1')] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb new file mode 100644 index 0000000000..0bd9d6514d --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d986252036 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From 96439e0f308537296b6ee2433077c95754ae5924 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 16:43:31 +0100 Subject: [PATCH 103/818] fix permissions on SWASH binaries --- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb | 2 ++ easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb | 2 ++ easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb index 59a30a98ae..767e04327d 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb @@ -21,6 +21,8 @@ parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb index dddde53b09..a9d434ebd1 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb @@ -21,6 +21,8 @@ parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb index c188883666..ad04f26f31 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb @@ -20,6 +20,8 @@ parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], -- GitLab From f99c2947bbf729e889e8bab045384248817dbe3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 16:59:41 +0100 Subject: [PATCH 104/818] fix typo in Qt5 patch description --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb | 2 ++ easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb | 2 ++ easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb | 2 ++ 4 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch index b9dfca8149..43f7c73fcc 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.1_fix-nan-inf.patch @@ -1,4 +1,4 @@ -fix compilation issue with Intel compilers: "error: more than one instance of overloaded function 'isnan'i matches the argument list" +fix compilation issue with Intel compilers: "error: more than one instance of overloaded function 'isnan' matches the argument list" author: Kenneth Hoste (HPC-UGent) --- ./qtbase/src/corelib/global/qnumeric_p.h.orig 2017-01-12 14:07:25.154941190 +0100 +++ ./qtbase/src/corelib/global/qnumeric_p.h 2017-01-12 14:08:03.841376056 +0100 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb index 59a30a98ae..767e04327d 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb @@ -21,6 +21,8 @@ parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb index dddde53b09..a9d434ebd1 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb @@ -21,6 +21,8 @@ parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb index c188883666..ad04f26f31 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb @@ -20,6 +20,8 @@ parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], -- GitLab From 0d028c1ce536f4b73b87bda686f4e92f46f04621 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 20:28:48 +0100 Subject: [PATCH 105/818] adding easyconfigs: Anaconda2-4.2.0.eb, Anaconda3-4.2.0.eb --- .../a/Anaconda2/Anaconda2-4.2.0.eb | 19 +++++++++++++++++++ .../a/Anaconda3/Anaconda3-4.2.0.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb new file mode 100644 index 0000000000..3fe1b814e4 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb @@ -0,0 +1,19 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda2' +version = '4.2.0' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['a0d1fbe47014b71c6764d76fb403f217'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb new file mode 100644 index 0000000000..9d27c79985 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb @@ -0,0 +1,19 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '4.2.0' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['4692f716c82deb9fa6b59d78f9f6e85c'] + +moduleclass = 'lang' -- GitLab From ddbe6019053f6234c01fd88eca5eb04e609c2d3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 20:47:51 +0100 Subject: [PATCH 106/818] bump to Anaconda 4.2.0, extend sanity check, style fixes --- easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb index d51a7c6584..2158bb874d 100644 --- a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb +++ b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb @@ -5,23 +5,24 @@ easyblock = 'Conda' -name = "QIIME" -version = "1.9.1" -variant = "Linux-x86_64" +name = 'QIIME' +version = '1.9.1' +variant = 'Linux-x86_64' homepage = 'http://qiime.org/' -description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.""" +description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis + from raw DNA sequencing data.""" toolchain = {'name': 'dummy', 'version': ''} -requirements = "python=2.7 %(namelower)s=%(version)s matplotlib=1.4.3 mock nose" +requirements = "%(namelower)s=%(version)s matplotlib=1.4.3 mock nose" channels = ['bioconda'] -builddependencies = [('Anaconda2', '4.0.0')] +builddependencies = [('Anaconda2', '4.2.0')] sanity_check_paths = { 'files': ['bin/print_qiime_config.py'], - 'dirs': [] + 'dirs': ['lib/python2.7/site-packages/qiime'] } sanity_check_commands = ['print_qiime_config.py -t'] -- GitLab From ad2cf31f833bd76cc46ed319fe34c5fc7adf6493 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 20:53:46 +0100 Subject: [PATCH 107/818] remove unused 'variant' --- easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb index 2158bb874d..401987f750 100644 --- a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb +++ b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb @@ -7,7 +7,6 @@ easyblock = 'Conda' name = 'QIIME' version = '1.9.1' -variant = 'Linux-x86_64' homepage = 'http://qiime.org/' description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis -- GitLab From d332250d90e6ed5f88cec41237206f495fdab34c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Jan 2017 21:36:14 +0100 Subject: [PATCH 108/818] clean up dependency specs in GroIMP easyconfig --- easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb index 3b5abf3832..d86f8fea57 100644 --- a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb +++ b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb @@ -12,10 +12,10 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['GroIMP-%(version)s-src.zip'] dependencies = [ - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112'), ] -builddependencies = [('ant', '1.10.0', '-Java-%(javaver)s', True)] +builddependencies = [('ant', '1.10.0', '-Java-%(javaver)s')] install_cmd = 'cd %(name)s-%(version)s/Build && ant && cp -a ../app/* %(installdir)s/' -- GitLab From 55fd84bf99acf667c597b349c1a45a55f15ece03 Mon Sep 17 00:00:00 2001 From: jerowe Date: Fri, 13 Jan 2017 08:23:46 +0400 Subject: [PATCH 109/818] adding channel to perl-app-cpanminus --- .../p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb index c89d3af9f2..cc1d205d40 100644 --- a/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb @@ -22,7 +22,7 @@ description = """ cpanm - get, unpack build and install modules from CPAN """ toolchain = {'name': 'dummy', 'version': ''} requirements = "%(name)s=%(version)s" -channels = ['bioconda'] +channels = ['bioconda', 'conda-forge'] builddependencies = [('Anaconda2', '4.0.0')] -- GitLab From c03f555c6b2152db21cb50ad8389282a0c0c7d11 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 13 Jan 2017 09:05:20 +0100 Subject: [PATCH 110/818] Add alternate URL to avoid breaking with new upstream releases --- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb index ad22d09979..0d6ccf3dc7 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -18,7 +18,11 @@ description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] + sources = [SOURCE_TAR_GZ] patches = ['EMBOSS_disable-embossupdate.patch'] -- GitLab From 20a9daa3f271ce1b150bd2349db87b90943c6b8a Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Fri, 13 Jan 2017 09:55:13 +0000 Subject: [PATCH 111/818] Adding tmux 2.3 and libevent 2.0.22 with toolchain (GCC-5.4.0-2.26) --- .../libevent-2.0.22-GCC-5.4.0-2.26.eb | 23 +++++++++++++++ .../t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb | 29 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..bde8a2eca6 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb @@ -0,0 +1,23 @@ +# Automatically converted from libevent-2.0.22-GCCcore-5.4.0.eb +# by /gpfs/sysapps/bham/scripts/easybuild/recursive_build_with_new_toolchain.py +# Automatically converted from libevent-2.0.22-GCCcore-4.9.3.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.0.22' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = [ + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', +] + +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..81ddd2f6b3 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb @@ -0,0 +1,29 @@ +# Automatically converted from tmux-2.3-GCCcore-5.4.0.eb +# by /gpfs/sysapps/bham/scripts/easybuild/recursive_build_with_new_toolchain.py +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.3' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily between +several programs in one terminal, detach them (they keep running in the background) +and reattach them to a different terminal.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 64437d4118c1ba2c35902f01b3eaff24605f3f05 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Fri, 13 Jan 2017 10:00:52 +0000 Subject: [PATCH 112/818] Tidying up UoB comments --- .../easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb | 4 ---- easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb | 2 -- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb index bde8a2eca6..e069d2a221 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb @@ -1,7 +1,3 @@ -# Automatically converted from libevent-2.0.22-GCCcore-5.4.0.eb -# by /gpfs/sysapps/bham/scripts/easybuild/recursive_build_with_new_toolchain.py -# Automatically converted from libevent-2.0.22-GCCcore-4.9.3.eb -# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py easyblock = 'ConfigureMake' name = 'libevent' diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb index 81ddd2f6b3..185b4711a6 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb @@ -1,5 +1,3 @@ -# Automatically converted from tmux-2.3-GCCcore-5.4.0.eb -# by /gpfs/sysapps/bham/scripts/easybuild/recursive_build_with_new_toolchain.py easyblock = 'ConfigureMake' name = 'tmux' -- GitLab From 5bebbc71a1bec819c4c0c92286c75e323c066810 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 11:47:39 +0100 Subject: [PATCH 113/818] {data}[intel/2016b] GDAL v2.1.2 --- .../GDAL-2.1.2-intel-2016b-Python-2.7.12.eb | 51 +++++++++++++++++++ .../g/GDAL/GDAL-2.1.2_fix-vrtsources.patch | 20 ++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.2_fix-vrtsources.patch diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9e5b8f7b62 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +patches = ['GDAL-%(version)s_fix-vrtsources.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +# there is a bug in the build system causing the build with libtool to fail for the moment +# (static library is also missing because of this) +configopts += ' --without-libtool' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2_fix-vrtsources.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2_fix-vrtsources.patch new file mode 100644 index 0000000000..238de86030 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2_fix-vrtsources.patch @@ -0,0 +1,20 @@ +fix compilation issue, cfr. https://trac.osgeo.org/gdal/ticket/6748 +Index: /trunk/gdal/frmts/vrt/vrtsources.cpp +=================================================================== +--- /trunk/gdal/frmts/vrt/vrtsources.cpp (revision 36798) ++++ /trunk/gdal/frmts/vrt/vrtsources.cpp (revision 36799) +@@ -2592,4 +2592,14 @@ + } + ++// Explicitly instantiate template method, as it is used in another file. ++template ++CPLErr VRTComplexSource::RasterIOInternal( int nReqXOff, int nReqYOff, ++ int nReqXSize, int nReqYSize, ++ void *pData, int nOutXSize, int nOutYSize, ++ GDALDataType eBufType, ++ GSpacing nPixelSpace, GSpacing nLineSpace, ++ GDALRasterIOExtraArg* psExtraArg, ++ GDALDataType eWrkDataType ); ++ + /************************************************************************/ + /* GetMinimum() */ -- GitLab From bd835b55ce17a95ac3da380c62c48f84c923db22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 14:23:39 +0100 Subject: [PATCH 114/818] adding easyconfigs: libspatialindex-1.8.5-intel-2016b.eb --- .../libspatialindex-1.8.5-intel-2016b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-intel-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-intel-2016b.eb new file mode 100644 index 0000000000..04f41e27d3 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-intel-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialindex' +version = '1.8.5' + +homepage = 'http://libspatialindex.github.io' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/libspatialindex/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.a', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' -- GitLab From a7c7c49339783f240a01113c647f5d8215e2f817 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 14:32:03 +0100 Subject: [PATCH 115/818] adding easyconfigs: GATK-3.7-Java-1.8.0_112.eb --- .../g/GATK/GATK-3.7-Java-1.8.0_112.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb new file mode 100644 index 0000000000..a82a27cc92 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +dependencies = [('Java', '1.8.0_112')] + +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From 5c005d5daae69dad56e1a79e98173a3ff6230d37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 14:49:14 +0100 Subject: [PATCH 116/818] adding easyconfigs: PyQt5-5.7.1-intel-2016b-Python-2.7.12.eb, PyQt-4.12-intel-2016b-Python-2.7.12.eb, SIP-4.19-intel-2016b-Python-2.7.12.eb --- .../PyQt-4.12-intel-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ .../PyQt5-5.7.1-intel-2016b-Python-2.7.12.eb | 34 +++++++++++++++++ .../SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.7.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9ea42178d7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] +sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('SIP', '4.19', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..81482a92b2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] +sources = ['%(name)s_gpl-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('SIP', '4.19', versionsuffix), + ('Qt5', '5.7.1'), +] + +configopts = "configure.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9f5fa19c24 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.12')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 7e2223f80cf40ee2cf482eb646c61fb3c099c062 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 16:06:14 +0100 Subject: [PATCH 117/818] adding easyconfigs: QwtPolar-1.1.1-intel-2016b.eb, Qwt-6.1.3-intel-2016b.eb --- .../q/Qwt/Qwt-6.1.3-intel-2016b.eb | 29 +++++++++++++++++++ .../q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-intel-2016b.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-intel-2016b.eb new file mode 100644 index 0000000000..a477b16bef --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.3' + +homepage = 'http://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qt', '4.8.7'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@QWT_INSTALL_PREFIX[ ]*=.*@QWT_INSTALL_PREFIX = %(installdir)s@g' qwtconfig.pri && " +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb new file mode 100644 index 0000000000..8162f0b889 --- /dev/null +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'QwtPolar' +version = '1.1.1' + +homepage = 'http://qwtpolar.sourceforge.net/' +description = "The QwtPolar library contains classes for displaying values on a polar coordinate system." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qwt', '6.1.3'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@\\(QWT_POLAR_INSTALL_PREFIX[ ]*=\\).*@\\1 %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " +prebuildopts += "qmake qwtpolar.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwtpolar.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' -- GitLab From 6f4d6570da5cbbb163ac8f58907ca9f92b2f4605 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 16:06:35 +0100 Subject: [PATCH 118/818] adding easyconfigs: QCA-2.1.0-intel-2016b.eb --- .../q/QCA/QCA-2.1.0-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb new file mode 100644 index 0000000000..73895f04cb --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.0' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://delta.affinix.com/download/qca/2.0/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.1') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From 269ce401b0b9b52b1c3f850d6bb265509a6cc3cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 16:27:25 +0100 Subject: [PATCH 119/818] fix prebuildopts in QwtPolar easyconfig --- easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb index 8162f0b889..0b5d5c5c98 100644 --- a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb @@ -17,7 +17,7 @@ dependencies = [ skipsteps = ['configure'] -prebuildopts = "sed -i 's@\\(QWT_POLAR_INSTALL_PREFIX[ ]*=\\).*@\\1 %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts = r"sed -i 's@\(QWT_POLAR_INSTALL_PREFIX[ ]*=\).*@\1 %(installdir)s@g' qwtpolarconfig.pri && " prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " prebuildopts += "qmake qwtpolar.pro && " -- GitLab From b743638d3ac4dafa60f75ffc3edc64d79e15a812 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 16:48:58 +0100 Subject: [PATCH 120/818] fix sed command in QwtPolar easyconfig --- easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb index 0b5d5c5c98..4b8e6389ed 100644 --- a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-intel-2016b.eb @@ -17,7 +17,7 @@ dependencies = [ skipsteps = ['configure'] -prebuildopts = r"sed -i 's@\(QWT_POLAR_INSTALL_PREFIX[ ]*=\).*@\1 %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts = "sed -i 's@INSTALL_PREFIX[ ]*=.*@INSTALL_PREFIX = %(installdir)s@g' qwtpolarconfig.pri && " prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " prebuildopts += "qmake qwtpolar.pro && " -- GitLab From 483b832f0732c96972684c1f804d3bf1d88b4f73 Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Fri, 13 Jan 2017 17:03:47 +0100 Subject: [PATCH 121/818] easyconfig for ALPS 2.3 --- ...3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb | 43 +++++++++++++++++++ ....3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb | 43 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb new file mode 100644 index 0000000000..e9e9920e54 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' +separate_build_dir = True + +name = 'ALPS' +version = '2.3.0' +cxxstd = 'c++03' + +homepage = "http://alps.comp-phys.org/" +description = "ALPS project" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': cxxstd} + + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases/'] + +patches = [ + #'ALPS-find-python.patch' +] + +boostver = '1.63.0' +pyver = '2.7.12' + +dependencies = [ + ('CMake', '3.6.2'), + ('Boost', boostver, '-Python-%s' % (pyver)), + ('HDF5', '1.8.17', '-threadsafe') +] +versionsuffix='-Python-%s' % (pyver,) + +modextravars = { + 'ALPS_ROOT': '$root', +} +modextrapaths = { + 'PYTHONPATH': ['lib/'] +} + +sanity_check_paths={ + 'files': ['lib/libalps.so'], + 'dirs': ['include/alps', 'bin/', 'share/'], +} + diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb new file mode 100644 index 0000000000..42ed52aa98 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' +separate_build_dir = True + +name = 'ALPS' +version = '2.3.0' +cxxstd = 'c++03' + +homepage = "http://alps.comp-phys.org/" +description = "ALPS project" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': cxxstd} + + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases/'] + +patches = [ + #'ALPS-find-python.patch' +] + +boostver = '1.63.0' +pyver = '3.5.2' + +dependencies = [ + ('CMake', '3.6.2'), + ('Boost', boostver, '-Python-%s' % (pyver)), + ('HDF5', '1.8.17', '-threadsafe') +] +versionsuffix='-Python-%s' % (pyver,) + +modextravars = { + 'ALPS_ROOT': '$root', +} +modextrapaths = { + 'PYTHONPATH': ['lib/'] +} + +sanity_check_paths={ + 'files': ['lib/libalps.so'], + 'dirs': ['include/alps', 'bin/', 'share/'], +} + -- GitLab From 37ac3a952e49d5306d04df3bbf947c77685182ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 17:43:05 +0100 Subject: [PATCH 122/818] adding easyconfigs: buildenv-default-intel-2016b.eb --- .../b/buildenv/buildenv-default-intel-2016b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2016b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2016b.eb new file mode 100644 index 0000000000..4e742815d3 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2016b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +moduleclass = 'devel' -- GitLab From f4d728d6baba47763b4036bda9c97e5534d80579 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Jan 2017 17:53:31 +0100 Subject: [PATCH 123/818] adding easyconfigs: ImageJ-1.5.1i.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb new file mode 100644 index 0000000000..1ae33a127b --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.5.1i' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://imagej.nih.gov/ij/download/src/'] +sources = ['ij%s-src.zip' % ''.join(version.split('.'))] + +dependencies = [ + ('Java', '1.8.0_112'), +] + +builddependencies = [('ant', '1.10.0', '-Java-%(javaver)s')] + +install_cmd = 'cd source && ant build && cp ij.jar %(installdir)s' + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': [], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar'\n" + +moduleclass = 'tools' -- GitLab From dd44316940189bfcc6e90b9112fc64d1c4990871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Jan 2017 14:18:16 +0100 Subject: [PATCH 124/818] fix remarks --- .../easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb index ffcf5b339a..b188df034a 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb @@ -19,18 +19,16 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] -sources = ['elpa-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [('Autotools', '20150215')] -configopts = '--with-generic-simple --disable-shared ' +configopts = '--with-generic-simple ' configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' -parallel = 1 - sanity_check_paths = { - 'files': ['lib/libelpa.a'], + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT], 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], } -- GitLab From 8c3c2005db08531cf1c762ed50fffc4cca9d3e5d Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Mon, 16 Jan 2017 11:32:28 +0100 Subject: [PATCH 125/818] rely on standard hdf5 installation --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb | 2 +- .../a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb index e9e9920e54..afe31e914f 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb @@ -25,7 +25,7 @@ pyver = '2.7.12' dependencies = [ ('CMake', '3.6.2'), ('Boost', boostver, '-Python-%s' % (pyver)), - ('HDF5', '1.8.17', '-threadsafe') + ('HDF5', '1.8.17') ] versionsuffix='-Python-%s' % (pyver,) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb index 42ed52aa98..05b4d43414 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb @@ -25,7 +25,7 @@ pyver = '3.5.2' dependencies = [ ('CMake', '3.6.2'), ('Boost', boostver, '-Python-%s' % (pyver)), - ('HDF5', '1.8.17', '-threadsafe') + ('HDF5', '1.8.17') ] versionsuffix='-Python-%s' % (pyver,) -- GitLab From b65ec96a396442f073ebf31aed8d01b4d463e44d Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Mon, 16 Jan 2017 11:38:07 +0100 Subject: [PATCH 126/818] rename .eb files --- ...63-Python-2.7.12.eb => ALPS-2.3.0-foss-2016b-Python-2.7.12.eb} | 0 ...1.63-Python-3.5.2.eb => ALPS-2.3.0-foss-2016b-Python-3.5.2.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/ALPS/{ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb => ALPS-2.3.0-foss-2016b-Python-2.7.12.eb} (100%) rename easybuild/easyconfigs/a/ALPS/{ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb => ALPS-2.3.0-foss-2016b-Python-3.5.2.eb} (100%) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-2.7.12.eb rename to easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb similarity index 100% rename from easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Boost-1.63-Python-3.5.2.eb rename to easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb -- GitLab From 1592e0443934d28d594c0daec093d6beaecb6d59 Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Mon, 16 Jan 2017 11:55:28 +0100 Subject: [PATCH 127/818] comments on easyconfig --- .../ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 17 ++++++----------- .../ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 17 ++++++----------- 2 files changed, 12 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index afe31e914f..761e64b159 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -1,33 +1,28 @@ easyblock = 'CMakeMake' -separate_build_dir = True name = 'ALPS' version = '2.3.0' -cxxstd = 'c++03' +versionsuffix = '-Python-%(pyver)s' homepage = "http://alps.comp-phys.org/" description = "ALPS project" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'cstd': cxxstd} - +toolchainopts = {'cstd': 'c++03'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases/'] -patches = [ - #'ALPS-find-python.patch' -] - boostver = '1.63.0' pyver = '2.7.12' dependencies = [ ('CMake', '3.6.2'), - ('Boost', boostver, '-Python-%s' % (pyver)), + ('Boost', boostver, '-Python-%s' % pyver), ('HDF5', '1.8.17') ] -versionsuffix='-Python-%s' % (pyver,) + +separate_build_dir = True modextravars = { 'ALPS_ROOT': '$root', @@ -37,7 +32,7 @@ modextrapaths = { } sanity_check_paths={ - 'files': ['lib/libalps.so'], + 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index 05b4d43414..d0f392c12a 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -1,33 +1,28 @@ easyblock = 'CMakeMake' -separate_build_dir = True name = 'ALPS' version = '2.3.0' -cxxstd = 'c++03' +versionsuffix = '-Python-%(pyver)s' homepage = "http://alps.comp-phys.org/" description = "ALPS project" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'cstd': cxxstd} - +toolchainopts = {'cstd': 'c++03'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases/'] -patches = [ - #'ALPS-find-python.patch' -] - boostver = '1.63.0' pyver = '3.5.2' dependencies = [ ('CMake', '3.6.2'), - ('Boost', boostver, '-Python-%s' % (pyver)), + ('Boost', boostver, '-Python-%s' % pyver), ('HDF5', '1.8.17') ] -versionsuffix='-Python-%s' % (pyver,) + +separate_build_dir = True modextravars = { 'ALPS_ROOT': '$root', @@ -37,7 +32,7 @@ modextrapaths = { } sanity_check_paths={ - 'files': ['lib/libalps.so'], + 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } -- GitLab From 425715410423855576dddd41e53fcf9ed847fef0 Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Mon, 16 Jan 2017 13:13:59 +0100 Subject: [PATCH 128/818] fix pyver and cleanup boost version requirement --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 6 ++---- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 761e64b159..511a60b649 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -13,12 +13,10 @@ toolchainopts = {'cstd': 'c++03'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases/'] -boostver = '1.63.0' -pyver = '2.7.12' - dependencies = [ ('CMake', '3.6.2'), - ('Boost', boostver, '-Python-%s' % pyver), + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), ('HDF5', '1.8.17') ] diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index d0f392c12a..3f4a6a13cc 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -13,12 +13,10 @@ toolchainopts = {'cstd': 'c++03'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases/'] -boostver = '1.63.0' -pyver = '3.5.2' - dependencies = [ ('CMake', '3.6.2'), - ('Boost', boostver, '-Python-%s' % pyver), + ('Python', '3.5.2'), + ('Boost', '1.63.0', versionsuffix), ('HDF5', '1.8.17') ] -- GitLab From 8e6d07951faff6e957e304285452e62d9c0e6acd Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 Jan 2017 20:54:23 +0800 Subject: [PATCH 129/818] fix source_urls --- .../easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb index 17f6d6b14b..738e6ce0b1 100644 --- a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb +++ b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb @@ -27,7 +27,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # fi. http://www.slac.stanford.edu/~abh/bbcp/bin/amd64_linux26/bbcp # VERY poor way of distributing software sources = [name] -source_urls = [homepage + 'bin/%s' % versionsuffix] +source_urls = [homepage + 'bin/%s' % versionsuffix[1:]] sanity_check_paths = { 'files': ['bbcp'], -- GitLab From 86510f0c8be606a7f49438c8cb2462d8ba0366f4 Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Mon, 16 Jan 2017 15:29:41 +0100 Subject: [PATCH 130/818] moduleclass --- .../easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 1 + .../easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 511a60b649..352fbdaecb 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -34,3 +34,4 @@ sanity_check_paths={ 'dirs': ['include/alps', 'bin/', 'share/'], } +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index 3f4a6a13cc..36e392f1f5 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -34,3 +34,4 @@ sanity_check_paths={ 'dirs': ['include/alps', 'bin/', 'share/'], } +moduleclass = 'phys' -- GitLab From 4c721f56e5115cd3543ecba237d675d7465ae061 Mon Sep 17 00:00:00 2001 From: Michele Dolfi Date: Mon, 16 Jan 2017 15:32:35 +0100 Subject: [PATCH 131/818] description --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 5 ++++- .../easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 352fbdaecb..12d87fd3a6 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -5,7 +5,10 @@ version = '2.3.0' versionsuffix = '-Python-%(pyver)s' homepage = "http://alps.comp-phys.org/" -description = "ALPS project" +description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort + aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as + C++ libraries for simplifying the development of such code. +""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'cstd': 'c++03'} diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index 36e392f1f5..33dbe5c739 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -5,7 +5,10 @@ version = '2.3.0' versionsuffix = '-Python-%(pyver)s' homepage = "http://alps.comp-phys.org/" -description = "ALPS project" +description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort + aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as + C++ libraries for simplifying the development of such code. +""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'cstd': 'c++03'} -- GitLab From 7f1140260f630abf462ea7d2fd22f6581cd8240d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 Jan 2017 23:12:24 +0800 Subject: [PATCH 132/818] fix source_urls --- easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb index e9345ea16d..3c5b16c424 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """Google Protocol Buffers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://github.com/google/%(namelower)s/releases/download/v%(version)s/'] sanity_check_paths = { 'files': ['bin/protoc'], diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb index 56627b2c07..3dff68438e 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb @@ -9,7 +9,7 @@ description = """Google Protocol Buffers""" toolchain = {'name': 'goolf', 'version': '1.7.20'} sources = [SOURCE_TAR_GZ] -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://github.com/google/%(namelower)s/releases/download/v%(version)s/'] sanity_check_paths = { 'files': ['bin/protoc'], diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb index 7a7091bb5e..03255276d8 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb @@ -9,7 +9,7 @@ description = """Google Protocol Buffers""" toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCE_TAR_GZ] -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://github.com/google/%(namelower)s/releases/download/v%(version)s/'] sanity_check_paths = { 'files': ['bin/protoc'], -- GitLab From 357b8b4e33a3a6c1b6f6aa5a23c54cf650f4966a Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Jan 2017 16:39:45 +0000 Subject: [PATCH 133/818] Updating source URL for tmux 1.9a --- easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index 8b0f6b51a8..5cd890962a 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = [SOURCEFORGE_SOURCE] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] dependencies = [ ('ncurses', '5.9'), -- GitLab From 19068af8a78935721b751058523e6406fcecff9d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2017 11:34:38 +0100 Subject: [PATCH 134/818] adding easyconfigs: libpthread-stubs-0.3-intel-2016b.eb --- .../libpthread-stubs-0.3-intel-2016b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb new file mode 100755 index 0000000000..132a89cd1e --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016b'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 3c0acff06c34ff6fd14a021dee6830baabe5202e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2017 11:49:50 +0100 Subject: [PATCH 135/818] adding easyconfigs: xorg-macros-1.19.0-foss-2016b.eb, xorg-macros-1.19.0-intel-2016b.eb --- .../xorg-macros-1.19.0-foss-2016b.eb | 24 +++++++++++++++++++ .../xorg-macros-1.19.0-intel-2016b.eb | 22 +++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100755 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb create mode 100755 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb new file mode 100755 index 0000000000..2e98d1a81e --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +osdependencies = [('perl-Thread-Queue', 'libthread-queue-any-perl')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb new file mode 100755 index 0000000000..52e3d066e8 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From de4c91b4da9ed4b5001afc5301ef059eacf38c6e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2017 11:58:01 +0100 Subject: [PATCH 136/818] adding easyconfigs: libpciaccess-0.13.4-foss-2016b.eb, libpciaccess-0.13.4-intel-2016b.eb --- .../libpciaccess-0.13.4-foss-2016b.eb | 26 +++++++++++++++++++ .../libpciaccess-0.13.4-intel-2016b.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100755 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb create mode 100755 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb new file mode 100755 index 0000000000..11ed8ea67d --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016b'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb new file mode 100755 index 0000000000..9124b553ab --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016b'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' -- GitLab From f62b9d2864692d797a1598c96270adaf63db0c16 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2017 12:03:42 +0100 Subject: [PATCH 137/818] adding easyconfigs: libdrm-2.4.70-foss-2016b.eb, libdrm-2.4.70-intel-2016b.eb --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb | 2 ++ easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb index 5d9e8ac938..bd2875fe53 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} dependencies = [ ('X11', '20160819'), + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb index 9fb07a2954..1f6c3d5a42 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} dependencies = [ ('X11', '20160819'), + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.4'), ] sanity_check_paths = { -- GitLab From 23bd5e9481be54b792b52d6fd9f7ffa118a30740 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2017 12:27:36 +0100 Subject: [PATCH 138/818] adding easyconfigs: libpthread-stubs-0.3-foss-2016b.eb --- .../libpthread-stubs-0.3-foss-2016b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb new file mode 100755 index 0000000000..3f5229b135 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016b'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 7e8ab9e466ae87002b5783a7ce596100f7fabd1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 17 Jan 2017 12:47:40 +0100 Subject: [PATCH 139/818] removed unnecessary escaping of $ in modloadmsg --- .../c/cramtools/cramtools-2.0-Java-1.7.0_80.eb | 2 +- .../c/cramtools/cramtools-3.0-Java-1.7.0_80.eb | 2 +- .../DicomBrowser-1.7.0b5-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/f/findhap/findhap-4.eb | 12 ++++++------ easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb | 2 +- .../easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb | 2 +- .../easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb | 2 +- .../easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb | 2 +- .../easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb | 2 +- .../easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 2 +- .../easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 2 +- .../easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb | 2 +- .../easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb | 2 +- .../easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb | 2 +- .../easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb | 2 +- easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb | 2 +- .../jModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 2 +- ...Test-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 2 +- .../m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb | 2 +- .../m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 2 +- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 2 +- .../p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 4 ++-- .../p/picard/picard-2.0.1-Java-1.8.0_66.eb | 2 +- .../p/picard/picard-2.1.0-Java-1.8.0_74.eb | 2 +- .../p/picard/picard-2.1.1-Java-1.8.0_112.eb | 2 +- .../p/picard/picard-2.1.1-Java-1.8.0_74.eb | 2 +- .../p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb | 2 +- .../t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb | 4 ++-- .../easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 4 ++-- .../easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb | 4 ++-- .../v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- .../v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 2 +- .../easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 2 +- .../easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 2 +- 37 files changed, 46 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index d2027312f5..c4b4b9a935 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -19,7 +19,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar ${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb index d00a912e71..12fc50e105 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/enasequence/%(name)s/archive/'] dependencies = [('Java', '1.7.0_80')] -modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar ${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 295844b8ba..0a71b94670 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -26,6 +26,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """To execute run: java -jar \\$EBROOTDICOMBROWSER/%(name)s-%(version)s-bin-with-dependencies.jar""" +modloadmsg = """To execute run: java -jar $EBROOTDICOMBROWSER/%(name)s-%(version)s-bin-with-dependencies.jar""" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/findhap/findhap-4.eb b/easybuild/easyconfigs/f/findhap/findhap-4.eb index 06eb1f492a..7622374b66 100644 --- a/easybuild/easyconfigs/f/findhap/findhap-4.eb +++ b/easybuild/easyconfigs/f/findhap/findhap-4.eb @@ -20,14 +20,14 @@ modextrapaths = { modloadmsg = """ Copy the following file to the directory from which you will be running the executable: -\\$EBROOTFINDHAP/findhap.options +$EBROOTFINDHAP/findhap.options -Other files in the \\$EBROOTFINDHAP directory are: +Other files in the $EBROOTFINDHAP directory are: -\\$EBROOTFINDHAP/genotypes.txt -\\$EBROOTFINDHAP/chromosome.data -\\$EBROOTFINDHAP/pedigree.file -\\$EBROOTFINDHAP/sequences.readdepth +$EBROOTFINDHAP/genotypes.txt +$EBROOTFINDHAP/chromosome.data +$EBROOTFINDHAP/pedigree.file +$EBROOTFINDHAP/sequences.readdepth """ sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index dd2c25a627..8fd2e29e7b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -16,7 +16,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index ee70681358..ee1fea2c11 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index dde93eb10a..549fa91f1b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index a45cb4ec3b..a55a0d1b45 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 1bdef83c68..3ed2ad06c3 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -16,7 +16,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index 21448792b2..3af4b8acdd 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 38e7ae6db1..5b4401c174 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_21' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index 689accfbd9..aa2cb8839c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index 520cb6b37a..65f9083180 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -32,7 +32,7 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index adf96fa7cf..76a7aaf5f7 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -32,7 +32,7 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index c52824dc92..098e5e229b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -30,7 +30,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.8.0_74')] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index 3bbed9824e..312f7889cf 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -32,7 +32,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.8.0_92')] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb index d86f8fea57..aff38f5ddf 100644 --- a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb +++ b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use GroIMP: java -jar \\$EBROOTGROIMP/core.jar\n" +modloadmsg = "To use GroIMP: java -jar $EBROOTGROIMP/core.jar\n" moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 00bc8cb97d..48c4450932 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -26,7 +26,7 @@ dependencies = [ install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" -modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" +modloadmsg = """To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar""" sanity_check_paths = { 'files': ['jModelTest.jar'], diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index 91946b388e..334b79cc72 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -26,7 +26,7 @@ dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" -modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" +modloadmsg = """To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar""" sanity_check_paths = { 'files': ['jModelTest.jar'], diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index 35b0a5d11b..e0545e68bf 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -24,7 +24,7 @@ sanity_check_paths = { modextrapaths = {'CLASSPATH': 'libs/*'} -modloadmsg = """To execute MATSim GUI: java -jar \\${EBROOTMATSIM}/%(namelower)s-%(version)s.jar +modloadmsg = """To execute MATSim GUI: java -jar ${EBROOTMATSIM}/%(namelower)s-%(version)s.jar To execute MATSim in batch mode: java org.matsim.run.Controller You might have to adjust the requested memory""" diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index afe163b841..8df6938bda 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -30,7 +30,7 @@ sanity_check_paths = { } modloadmsg = """ -to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 0d2d28d47b..9292c46b7d 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -31,7 +31,7 @@ sanity_check_paths = { } modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +To start MuTect: java -jar $EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb index 86bd5019e2..a2300aabe6 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -32,7 +32,7 @@ sanity_check_paths = { } modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/%(namelower)s-%(version)s.jar +To start MuTect: java -jar $EBROOTMUTECT/%(namelower)s-%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 4071bc769a..dd5eb01734 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -27,8 +27,8 @@ sanity_check_paths = { } modloadmsg = """ -To execute GUI run: java -Xmx1024m -Xms512m -jar \\$EBROOTPGDSPIDER/PGDSpider2.jar -To execute CLI run: java -Xmx1024m -Xms512m -jar \\$EBROOTPGDSPIDER/PGDSpider2-cli.jar +To execute GUI run: java -Xmx1024m -Xms512m -jar $EBROOTPGDSPIDER/PGDSpider2.jar +To execute CLI run: java -Xmx1024m -Xms512m -jar $EBROOTPGDSPIDER/PGDSpider2-cli.jar Adjust memory according to your requirements""" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 742c2507d1..7aa145e449 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb index 88bda5b21f..d9b82dd722 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb index 9ac8383024..67c7abf4fe 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_112')] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb index b7bb2304d4..b570418566 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_74')] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb index a9b5ed1e23..9487e24fd4 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb @@ -34,6 +34,6 @@ sanity_check_paths = { 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], } -modloadmsg = "prokka scripts are located in \\$EBROOTPROKKA/bin; databases are located in \\$EBROOTPROKKA/db" +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb index a89bd3216a..33547a587c 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb @@ -23,7 +23,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute Trimmomatic run: java -jar \\$EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" +modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" sanity_check_paths = { 'files': ["trimmomatic-%(version)s.jar"], diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb index 1f3105220a..02d5fea5de 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb @@ -17,9 +17,9 @@ preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " # This will overwrite a users $TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" -modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index e8a270b38c..c524f85857 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -17,9 +17,9 @@ preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " # This will overwrite a users $TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" -modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb index 0eff73d3cc..a4b5f9fb26 100755 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb @@ -17,9 +17,9 @@ preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " # This will overwrite a users $TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" -modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index ba30d5877f..8ae2ef6c24 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -24,7 +24,7 @@ sanity_check_paths = { } modloadmsg = """ -to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +to execute: java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 186dfc58cc..53aad96768 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -24,7 +24,7 @@ sanity_check_paths = { } modloadmsg = """ -to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +to execute: java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index a65ca2295b..f5c3467ae4 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -35,6 +35,6 @@ modextravars = { 'WEKAINSTALL': '$root', } -modloadmsg = " execute WEKA: java -jar \\$EBROOTWEKA/weka.jar " +modloadmsg = " execute WEKA: java -jar $EBROOTWEKA/weka.jar " moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 396230d2a7..579709769c 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -35,6 +35,6 @@ modextravars = { 'WEKAINSTALL': '$root', } -modloadmsg = " execute WEKA: java -jar \\$EBROOTWEKA/weka.jar " +modloadmsg = " execute WEKA: java -jar $EBROOTWEKA/weka.jar " moduleclass = 'bio' -- GitLab From b554480c60317bcba96cec42c7a71f1772ff339e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 17 Jan 2017 12:55:36 +0100 Subject: [PATCH 140/818] removed curly braces in modloadmsg they shouldn't be needed here --- .../easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb | 2 +- .../easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb | 2 +- .../m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index c4b4b9a935..bcfd3d6103 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -19,7 +19,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute cramtools run: java -jar ${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb index 12fc50e105..f8e71d5dc1 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/enasequence/%(name)s/archive/'] dependencies = [('Java', '1.7.0_80')] -modloadmsg = "To execute cramtools run: java -jar ${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index e0545e68bf..421c8d4540 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -24,7 +24,7 @@ sanity_check_paths = { modextrapaths = {'CLASSPATH': 'libs/*'} -modloadmsg = """To execute MATSim GUI: java -jar ${EBROOTMATSIM}/%(namelower)s-%(version)s.jar +modloadmsg = """To execute MATSim GUI: java -jar $EBROOTMATSIM/%(namelower)s-%(version)s.jar To execute MATSim in batch mode: java org.matsim.run.Controller You might have to adjust the requested memory""" diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 7aa145e449..1e2e1290f3 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb index d9b82dd722..73072b689d 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb index 67c7abf4fe..a11a884ac1 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_112')] -modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb index b570418566..ad5c8d1dbb 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_74')] -modloadmsg = "To execute picard run: java -jar ${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" moduleclass = 'bio' -- GitLab From 7ae3cbc903d9a35bb37c5217b892a11129a77149 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 17 Jan 2017 13:55:38 +0100 Subject: [PATCH 141/818] unified string formatting changed mutliple modloadmsg to one multiline modloadmsg added new lines at the end of modloadmsg changed triple quotes to single quotes for single line strings --- easybuild/easyconfigs/a/ADF/ADF-2014.02.eb | 7 ++++--- .../easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb | 7 ++++--- easybuild/easyconfigs/a/ADF/ADF-2016.101.eb | 7 ++++--- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 3 +-- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 3 +-- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 3 +-- .../CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- .../CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb | 2 +- .../easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb | 2 +- .../easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb | 2 +- .../d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb | 2 +- easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb | 2 +- .../jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 2 +- ...jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 3 ++- .../easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb | 4 +--- .../easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 4 +--- .../easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 4 +--- .../p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 3 ++- .../easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb | 2 +- .../easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb | 2 +- .../easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb | 2 +- .../easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb | 2 +- .../p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb | 2 +- .../t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb | 2 +- .../u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb | 3 ++- .../easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb | 3 ++- .../easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb | 3 ++- .../easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 4 +--- .../easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 4 +--- easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 2 +- 47 files changed, 61 insertions(+), 68 deletions(-) diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb index 045e5244fd..f7098831f6 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb @@ -24,8 +24,9 @@ modextravars = { 'ADFRESOURCES': '%(installdir)s/atomicdata', } -modloadmsg = "These environment variables need to be defined before using ADF:\n" -modloadmsg += " * $SCMLICENSE: path to ADF license file\n" -modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" +modloadmsg = """These environment variables need to be defined before using ADF: + * $SCMLICENSE: path to ADF license file + * $SCM_TMPDIR: path to user scratch directory +""" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb index 21843552e8..a094b11d6d 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb @@ -15,8 +15,9 @@ sources = [ license_file = HOME + "/licenses/ADF/license.txt" -modloadmsg = "These environment variables need to be defined before using ADF:\n" -modloadmsg += " * $SCMLICENSE: path to ADF license file\n" -modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" +modloadmsg = """These environment variables need to be defined before using ADF: + * $SCMLICENSE: path to ADF license file + * $SCM_TMPDIR: path to user scratch directory +""" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb index 5fe5e14c14..6c3aae4360 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb @@ -24,8 +24,9 @@ modextravars = { 'ADFRESOURCES': '%(installdir)s/atomicdata', } -modloadmsg = "These environment variables need to be defined before using ADF:\n" -modloadmsg += " * $SCMLICENSE: path to ADF license file\n" -modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" +modloadmsg = """These environment variables need to be defined before using ADF: + * $SCMLICENSE: path to ADF license file + * $SCM_TMPDIR: path to user scratch directory +""" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index cd21d99d6d..77fe6be1c2 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -30,7 +30,6 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the - compiled jni C code.""" +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index dff5ba78e2..1a60a0011d 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -30,7 +30,6 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the - compiled jni C code.""" +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 539e3c2d20..014d3f2635 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -28,7 +28,6 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the - compiled jni C code.""" +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index f2ca68b5c1..961eb91738 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -37,7 +37,6 @@ installopts = '-override compiler' host_compilers = ["icpc", "g++"] # Be careful and have a message consistent with the generated wrappers -modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" -modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created.\n" moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 8ed8a29bfc..5b078fe902 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -37,7 +37,6 @@ installopts = '-override compiler' host_compilers = ["icpc", "g++"] # Be careful and have a message consistent with the generated wrappers -modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" -modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created.\n" moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index bcfd3d6103..5f652c0c86 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -19,7 +19,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar\n" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb index f8e71d5dc1..a560b37abe 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/enasequence/%(name)s/archive/'] dependencies = [('Java', '1.7.0_80')] -modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar\n" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index c378da306a..7a15e698bd 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -33,6 +33,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """Define OMP_NUM_THREADS or use the command line option --omp-num-threads=N when using this application""" +modloadmsg = "Define OMP_NUM_THREADS or use the command line option --omp-num-threads=N when using this application\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 0a71b94670..5106c4165f 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -26,6 +26,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """To execute run: java -jar $EBROOTDICOMBROWSER/%(name)s-%(version)s-bin-with-dependencies.jar""" +modloadmsg = "To execute run: java -jar $EBROOTDICOMBROWSER/%(name)s-%(version)s-bin-with-dependencies.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index 8fd2e29e7b..15da25496f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -16,7 +16,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index ee1fea2c11..6afbdb7b4c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index 549fa91f1b..921621187e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index a55a0d1b45..7e9f79abb8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 3ed2ad06c3..272836da19 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -16,7 +16,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index 3af4b8acdd..959d6f681a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 5b4401c174..69dadef3c7 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_21' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index aa2cb8839c..c8e83f1af6 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index 65f9083180..e60f317150 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -32,7 +32,7 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 76a7aaf5f7..47af207c6f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -32,7 +32,7 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index 098e5e229b..9faee44d8b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -30,7 +30,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.8.0_74')] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index 312f7889cf..fa068137af 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -32,7 +32,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.8.0_92')] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb index a82a27cc92..9d0b198d0f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -32,7 +32,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.8.0_112')] -modloadmsg = """To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb index faccbfa2f1..110b480923 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb @@ -28,7 +28,7 @@ modextrapaths = { 'PATH': '', } -modloadmsg = """ To execute IGV run igv.sh """ +modloadmsg = "To execute IGV run igv.sh\n" sanity_check_paths = { 'files': ["igv.sh"], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb index 444b68f2e7..f8dd5d79f2 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb @@ -28,7 +28,7 @@ modextrapaths = { 'PATH': '', } -modloadmsg = """ To execute IGV run igv.sh """ +modloadmsg = "To execute IGV run igv.sh\n" sanity_check_paths = { 'files': ["igv.sh"], diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 48c4450932..07eff74434 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -26,7 +26,7 @@ dependencies = [ install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" -modloadmsg = """To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar""" +modloadmsg = "To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar\n" sanity_check_paths = { 'files': ['jModelTest.jar'], diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index 334b79cc72..ecf1089f64 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -26,7 +26,7 @@ dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" -modloadmsg = """To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar""" +modloadmsg = "To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar\n" sanity_check_paths = { 'files': ['jModelTest.jar'], diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index 421c8d4540..f41f912592 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -26,6 +26,7 @@ modextrapaths = {'CLASSPATH': 'libs/*'} modloadmsg = """To execute MATSim GUI: java -jar $EBROOTMATSIM/%(namelower)s-%(version)s.jar To execute MATSim in batch mode: java org.matsim.run.Controller -You might have to adjust the requested memory""" +You might have to adjust the requested memory +""" moduleclass = 'cae' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index 8df6938bda..aa90066de8 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -29,8 +29,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 9292c46b7d..4774c63625 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -30,8 +30,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -To start MuTect: java -jar $EBROOTMUTECT/muTect-%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb index a2300aabe6..c8d608145e 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -31,8 +31,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -To start MuTect: java -jar $EBROOTMUTECT/%(namelower)s-%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index dd5eb01734..89ae4df712 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -29,6 +29,7 @@ sanity_check_paths = { modloadmsg = """ To execute GUI run: java -Xmx1024m -Xms512m -jar $EBROOTPGDSPIDER/PGDSpider2.jar To execute CLI run: java -Xmx1024m -Xms512m -jar $EBROOTPGDSPIDER/PGDSpider2-cli.jar -Adjust memory according to your requirements""" +Adjust memory according to your requirements +""" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 1e2e1290f3..1d6200df1a 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb index 73072b689d..80d1371c6d 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb index a11a884ac1..c0f8364e0a 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_112')] -modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb index ad5c8d1dbb..0e3b399591 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_74')] -modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb index 9487e24fd4..e50c9d60b6 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb @@ -34,6 +34,6 @@ sanity_check_paths = { 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], } -modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db" +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb index 33547a587c..091f914cb3 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb @@ -23,7 +23,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" +modloadmsg = "To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n" sanity_check_paths = { 'files': ["trimmomatic-%(version)s.jar"], diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb index 52e9495873..cc2a64b9ff 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb @@ -27,7 +27,8 @@ install_cmd += "chmod a+rx %(installdir)s/bin/*" modloadmsg = """USEARCH (32-bit) is licensed software but can be used for free by individuals when registered. A 64-bit version is - also available. For more information see http://www.drive5.com/usearch .""" + also available. For more information see http://www.drive5.com/usearch . +""" sanity_check_paths = { 'files': ['bin/%(namelower)s', 'bin/%(namelower)s61'], diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb index 961153d9b4..d2a22ed8a6 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb @@ -19,7 +19,8 @@ install_cmd += "chmod a+rx %(installdir)s/bin/%(namelower)s" modloadmsg = """USEARCH (32-bit) is licensed software but can be used for free by individuals when registered. A 64-bit version is - also available. For more information see http://www.drive5.com/usearch .""" + also available. For more information see http://www.drive5.com/usearch . +""" sanity_check_paths = { 'files': ['bin/%(namelower)s'], diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb index 07e180dab5..c09d3e96a2 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb @@ -19,7 +19,8 @@ install_cmd += "chmod a+rx %(installdir)s/bin/%(namelower)s" modloadmsg = """USEARCH (32-bit) is licensed software but can be used for free by individuals when registered. A 64-bit version is - also available. For more information see http://www.drive5.com/usearch .""" + also available. For more information see http://www.drive5.com/usearch . +""" sanity_check_paths = { 'files': ['bin/%(namelower)s'], diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index 8ae2ef6c24..af1032ae7a 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -23,8 +23,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -to execute: java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 53aad96768..dd6c6f31b0 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -23,8 +23,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -to execute: java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index f5c3467ae4..77fe169073 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -35,6 +35,6 @@ modextravars = { 'WEKAINSTALL': '$root', } -modloadmsg = " execute WEKA: java -jar $EBROOTWEKA/weka.jar " +modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 579709769c..70198200d8 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -35,6 +35,6 @@ modextravars = { 'WEKAINSTALL': '$root', } -modloadmsg = " execute WEKA: java -jar $EBROOTWEKA/weka.jar " +modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" moduleclass = 'bio' -- GitLab From 5468931c3189bb93d121281e1ed91cb4d3f28a74 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 10:24:06 +0800 Subject: [PATCH 142/818] fix source_urls --- easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb | 4 ++-- .../easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb | 4 ++-- .../easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb index b12575ef89..ce89a700f0 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -11,8 +11,8 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = [ - 'https://github.com/downloads/%(name)s/%(name)s/', - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', + 'https://downloads.sourceforge.net/project/levent/release-%(version)s-stable/', ] sources = ['%(name)s-%(version)s-stable.tar.gz'] diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb index 2de9d3663c..fe73b8ae70 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -11,8 +11,8 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = [ - 'https://github.com/downloads/%(name)s/%(name)s/', - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', + 'https://downloads.sourceforge.net/project/levent/release-%(version)s-stable/', ] sources = ['%(name)s-%(version)s-stable.tar.gz'] diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb index 3b555aa6f7..7f0cee0e30 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb @@ -11,8 +11,8 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = [ - 'https://github.com/downloads/%(name)s/%(name)s/', - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', + 'https://downloads.sourceforge.net/project/levent/release-%(version)s-stable/', ] sources = ['%(name)s-%(version)s-stable.tar.gz'] -- GitLab From 786a0c2936c353423311d1a437ef50dbae5a062d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 15:01:59 +0800 Subject: [PATCH 143/818] fix source_urls --- easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb | 2 +- easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb index ae08a0b454..8f18c08a6e 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb @@ -12,7 +12,7 @@ central piece of information. toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] -source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +source_urls = ['http://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] sanity_check_paths = { 'files': ["bin/mvn"], diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb index 642c9d91d2..e4b7cb5e43 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb @@ -12,7 +12,7 @@ central piece of information. toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] -source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +source_urls = ['http://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] sanity_check_paths = { 'files': ["bin/mvn"], -- GitLab From bad37d0fa9656f993d0be64e5e0e286eeb2a26ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 18 Jan 2017 08:05:26 +0100 Subject: [PATCH 144/818] broke long messages into multiple modloadmsg --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 3 ++- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 3 ++- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 3 ++- .../c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 ++- .../c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 ++- 5 files changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 77fe6be1c2..76e04042bc 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -30,6 +30,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.\n" +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index 1a60a0011d..d1646b7dbe 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -30,6 +30,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.\n" +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 014d3f2635..7e9be8c9b6 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -28,6 +28,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.\n" +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 961eb91738..50a365b60a 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -37,6 +37,7 @@ installopts = '-override compiler' host_compilers = ["icpc", "g++"] # Be careful and have a message consistent with the generated wrappers -modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created.\n" +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created.\n" moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 5b078fe902..dc4d389baf 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -37,6 +37,7 @@ installopts = '-override compiler' host_compilers = ["icpc", "g++"] # Be careful and have a message consistent with the generated wrappers -modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created.\n" +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created.\n" moduleclass = 'system' -- GitLab From d1a28d92026de4d8ed478f71a4ecc82a22f96450 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 15:12:29 +0800 Subject: [PATCH 145/818] fix source_urls --- easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb index e2411ef3f5..585ebb9932 100644 --- a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -14,7 +14,7 @@ description = """ splitRef splits a reference haplotype file into smaller files toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.sph.umich.edu/csg/yli/splitRef/download/'] +source_urls = ['http://csg.sph.umich.edu/yli/splitRef/download/'] sources = ['%s.V%s.tgz' % (name, version.replace(".", ""))] altver = version.replace('.', '') -- GitLab From 35601749f68efba7c3694db62bbcb59500a52d62 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 15:19:09 +0800 Subject: [PATCH 146/818] fix source_urls --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index fae61083b0..41b36d91f6 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -9,11 +9,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] -source_urls = [ - 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', - 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', - 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', -] +source_urls = ['http://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/'] dependencies = [('Java', '1.7.0_76')] -- GitLab From c6d1107cdab9e83e40b94df158a9f94746b86efe Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 15:25:33 +0800 Subject: [PATCH 147/818] fix source_urls --- easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb index 02bb809a0b..df836d072b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb @@ -11,7 +11,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'pic': True} -source_urls = ['http://zlib.net/'] +source_urls = ['http://zlib.net/fossils/'] sources = [SOURCELOWER_TAR_GZ] # need to take care of $CFLAGS ourselves with dummy toolchain -- GitLab From 8cef19803d6cea774b78ead9a6f8baf1dac2c948 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 15:30:10 +0800 Subject: [PATCH 148/818] fix source_urls --- easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb index ab9d5fd44f..84ff25e534 100644 --- a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb +++ b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb @@ -9,7 +9,7 @@ description = """Apache HBase. is the Hadoop database, a distributed, scalable, toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin.tar.gz'] -source_urls = ['http://www.us.apache.org/dist/hbase/hbase-%(version)s/'] +source_urls = ['http://archive.apache.org/dist/hbase/hbase-%(version)s/'] dependencies = [('Java', '1.7.0_80')] -- GitLab From 6dc37e464c7c71e44816da07d0aa770a1b8e7514 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 18 Jan 2017 09:05:53 +0100 Subject: [PATCH 149/818] Remove reference to unneeded patch --- easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb index f8e72d71f0..f487ac6f42 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb @@ -15,7 +15,6 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = [SOURCEFORGE_SOURCE] patches = [ -# 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -- GitLab From 5b22dd06775c59cee7df92e51073ef4839d9379b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 16:13:42 +0800 Subject: [PATCH 150/818] fix source_urls --- easybuild/easyconfigs/p/PCC/PCC-20131024.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb index c40392b771..4ba60f4784 100644 --- a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb +++ b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb @@ -18,9 +18,9 @@ description = """The compiler is based on the original Portable C Compiler by S. toolchain = {'name': 'dummy', 'version': ''} -# eg. http://pcc.ludd.ltu.se/ftp/pub/pcc/pcc-20131024.tgz +# eg. http://pcc.ludd.ltu.se/ftp/pub/pcc/2013/pcc-20131024.tgz sources = ['pcc-%(version)s.tgz'] -source_urls = ['http://pcc.ludd.ltu.se/ftp/pub/pcc/'] +source_urls = ['http://pcc.ludd.ltu.se/ftp/pub/pcc/2013/'] builddependencies = [ ('flex', '2.5.35'), -- GitLab From e84c91c96dd57762d945068d3102b887285914d7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 16:49:00 +0800 Subject: [PATCH 151/818] fix source_urls --- easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb b/easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb index ec3e8a22d5..631b1a8562 100644 --- a/easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb @@ -12,7 +12,7 @@ description = """S-Lang is a multi-platform programmer's library designed to all toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['slang-%(version)s.tar.gz'] -source_urls = ['http://www.jedsoft.org/releases/slang/'] +source_urls = ['http://www.jedsoft.org/releases/slang/old/'] sanity_check_paths = { 'files': ['include/slang.h', 'bin/slsh', 'lib/libslang.%s' % SHLIB_EXT], -- GitLab From 7abb9d8725d2a66fba1f7be7c03d3d7a5027f051 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2017 16:54:40 +0800 Subject: [PATCH 152/818] fix source_urls --- .../easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb index 7c1505061b..ad64b7cf37 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb @@ -9,7 +9,7 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = ['https://download.libsodium.org/libsodium/releases/old/'] sources = [SOURCE_TAR_GZ] sanity_check_paths = { -- GitLab From 67546ef1068e26713da475a69b4cbbca756b9b09 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Jan 2017 10:26:49 +0100 Subject: [PATCH 153/818] bump zlib to 1.2.11 --- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb | 2 +- ...b-1.2.10-GCCcore-6.3.0.eb => zlib-1.2.11-GCCcore-6.3.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/z/zlib/{zlib-1.2.10-GCCcore-6.3.0.eb => zlib-1.2.11-GCCcore-6.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index 27418ca0e7..9346ceba7e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.10'), + ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb similarity index 92% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb rename to easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb index 89be4a6599..a15fb20fe6 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.10-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'zlib' -version = '1.2.10' +version = '1.2.11' homepage = 'http://www.zlib.net/' description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, @@ -11,7 +11,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://zlib.net/'] +source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -- GitLab From 827747a42bec4b794eca184627410dfa3fbd9948 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Wed, 18 Jan 2017 11:21:41 +0000 Subject: [PATCH 154/818] Generalising source URLs with %(name)s --- easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index 5cd890962a..6125b3dd38 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] dependencies = [ ('ncurses', '5.9'), diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb index 391b43238f..bb013b1619 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb index 185b4711a6..f419b0b85c 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] dependencies = [ ('ncurses', '6.0'), -- GitLab From 8c148cc2e68d6f7e024de4824086ba29d1902745 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 18 Jan 2017 09:17:04 -0600 Subject: [PATCH 155/818] Added Perl 5.24.0 for GCC 5.4.0-2.26 toolchain --- .../p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 888 ++++++++++++++++++ 1 file changed, 888 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..78af957181 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -0,0 +1,888 @@ +name = 'Perl' +version = '5.24.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.61', { + 'source_tmpl': 'Config-General-2.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-2016060801.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.05', { + 'source_tmpl': 'DateTime-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.00', { + 'source_tmpl': 'DateTime-TimeZone-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4218', { + 'source_tmpl': 'Module-Build-0.4218.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.24', { + 'source_tmpl': 'Params-Validate-1.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.416', { + 'source_tmpl': 'List-MoreUtils-0.416.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.34', { + 'source_tmpl': 'DateTime-1.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-2.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), 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['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-0.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + 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['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.04', { + 'source_tmpl': 'Test-Version-2.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.002004', { + 'source_tmpl': 'Moo-2.002004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.058', { + 'source_tmpl': 'HTTP-Tiny-0.058.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-0.9917.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + }), + 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['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2011', { + 'source_tmpl': 'Canary-Stability-2011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 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['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY/'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.37', { + 'source_tmpl': 'XML-XPath-1.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.42', { + 'source_tmpl': 'Capture-Tiny-0.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-2.000003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-1.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', '3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.11', { + 'source_tmpl': 'List-AllUtils-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.007', { + 'source_tmpl': 'Test-Exception-LessClever-0.007.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.45', { + 'source_tmpl': 'Scalar-List-Utils-1.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1804', { + 'source_tmpl': 'Moose-2.1804.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-1.410.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9160', { + 'source_tmpl': 'CPANPLUS-0.9160.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-0.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-2.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), +] + +moduleclass = 'lang' -- GitLab From 93244e6d4678314f6290d3857914d6288bcff385 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 18 Jan 2017 09:17:40 -0600 Subject: [PATCH 156/818] Added OpenSSL 1.1.0c for GCC 5.4.0-2.26 toolchain --- .../OpenSSL/OpenSSL-1.1.0c-GCC-5.4.0-2.26.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0c-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0c-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0c-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..783abc638a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0c-GCC-5.4.0-2.26.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.1.0c' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +builddependencies = [('Perl', '5.24.0')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 2088ed70e60a6c48422605f581430f03c8ce276f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 19 Jan 2017 16:20:43 +0800 Subject: [PATCH 157/818] fix source_urls --- .../a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb | 4 ++-- .../easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb | 4 ++-- .../a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb | 4 ++-- .../easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb | 4 ++-- .../a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb | 4 ++-- .../easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb | 4 ++-- .../easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 2 +- .../g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb | 7 ++++--- easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb | 7 ++++--- easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb | 7 ++++--- easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb | 7 ++++--- easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb | 6 +++--- 17 files changed, 41 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb index 38638c65fb..0e77075c8a 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb @@ -10,8 +10,8 @@ description = """ARPACK is a collection of Fortran77 subroutines designed to sol toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb index e567606aa7..8d3a7eb7fe 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb @@ -9,8 +9,8 @@ description = """ARPACK is a collection of Fortran77 subroutines designed to sol toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb index 837fa583de..e75f54d2e1 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb @@ -10,8 +10,8 @@ description = """ARPACK is a collection of Fortran77 subroutines designed to sol toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb index 15e7a3b734..ce27a87097 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb @@ -9,8 +9,8 @@ description = """ARPACK is a collection of Fortran77 subroutines designed to sol toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb index 6388557ca2..0e9b24405d 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb @@ -10,8 +10,8 @@ description = """ARPACK is a collection of Fortran77 subroutines designed to sol toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] -sources = ['%(name)s_%(version)s.tar.gz'] +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb index 15bec194be..6104f116d8 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb @@ -9,8 +9,8 @@ description = """ARPACK is a collection of Fortran77 subroutines designed to sol toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] -sources = ['%(name)s_%(version)s.tar.gz'] +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index eb2d005b6f..582161abc9 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -15,7 +15,7 @@ description = """The ChIP-Seq software provides methods for the analysis of ChIP toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/%(version)s/'] +source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/1.5.1/'] sources = ['%(namelower)s.%(version)s.tar.gz'] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index dcbe783b38..0bc8d276f9 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -15,7 +15,7 @@ description = """The ChIP-Seq software provides methods for the analysis of ChIP toolchain = {'name': 'goolf', 'version': '1.7.20'} -source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/%(version)s/'] +source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/1.5.1/'] sources = ['%(namelower)s.%(version)s.tar.gz'] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb index 8aa2e7719b..578d17b6ae 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb @@ -10,7 +10,7 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} -source_urls = ["http://downloads.ghostscript.com/public/"] +source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] # expat, freetype and libpng are optional deps, diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb index bba320bc05..3347248cd1 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb @@ -21,9 +21,10 @@ to handle everything from small to very large projects with speed and efficiency toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. http://git-core.googlecode.com/files/git-1.7.12.tar.gz -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://git-core.googlecode.com/files'] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = "make configure && " dependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb index 4c4de49303..ce913425b7 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb @@ -21,9 +21,10 @@ description = """Git is a free and open source distributed version control syste toolchain = {'name': 'ictce', 'version': '5.3.0'} -# eg. http://git-core.googlecode.com/files/git-1.7.12.tar.gz -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://git-core.googlecode.com/files'] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = "make configure && " dependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb index a705caba43..c516d9d10a 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb @@ -22,9 +22,10 @@ to handle everything from small to very large projects with speed and efficiency toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://git-core.googlecode.com/files'] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = "make configure && " dependencies = [ ('cURL', '7.29.0'), diff --git a/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb index 6dfc4c5947..c9189d4325 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb @@ -21,9 +21,10 @@ description = """Git is a free and open source distributed version control syste to handle everything from small to very large projects with speed and efficiency.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://git-core.googlecode.com/files'] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = "make configure && " dependencies = [ ('cURL', '7.29.0'), diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb index e70401308c..37e2c7a024 100644 --- a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb @@ -8,8 +8,8 @@ homepage = 'http://lynx.isc.org/' toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://lynx.isc.org/release/'] -sources = ['%(name)s%(version)s.tar.bz2'] +source_urls = ['http://invisible-mirror.net/archives/lynx/tarballs/'] +sources = ['%(name)s%(version)srel.2.tar.bz2'] sanity_check_paths = { 'files': ['bin/lynx'], diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb index 2b02e64ab0..022bb67915 100644 --- a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb @@ -8,8 +8,8 @@ homepage = 'http://lynx.isc.org/' toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://lynx.isc.org/release/'] -sources = ['%(name)s%(version)s.tar.bz2'] +source_urls = ['http://invisible-mirror.net/archives/lynx/tarballs/'] +sources = ['%(name)s%(version)srel.2.tar.bz2'] sanity_check_paths = { 'files': ['bin/lynx'], diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb index c2f466b38e..ab727c8b4c 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'MEME' version = '4.8.0' -homepage = 'http://meme.nbcr.net/' +homepage = 'http://meme-suite.org/' description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate @@ -24,9 +24,9 @@ description = """The MEME Suite allows you to: * discover motifs using MEME, DRE toolchain = {'name': 'goolf', 'version': '1.4.10'} -# Download from eg. http://ebi.edu.au/ftp/software/MEME/4.8.0/meme_4.8.0.tar.gz +# Download from eg. http://meme-suite.org/meme-software/4.8.0/meme_4.8.0.tar.gz sources = ['meme_%(version)s.tar.gz'] -source_urls = ['http://ebi.edu.au/ftp/software/MEME/%(version)s'] +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] dependencies = [ ('libxml2', '2.9.1'), diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb index e039fb1fe5..c1658c0642 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'MEME' version = '4.8.0' -homepage = 'http://meme.nbcr.net/' +homepage = 'http://meme-suite.org' description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate @@ -25,9 +25,9 @@ description = """The MEME Suite allows you to: * discover motifs using MEME, DRE toolchain = {'name': 'ictce', 'version': '5.3.0'} -# Download from eg. http://ebi.edu.au/ftp/software/MEME/4.8.0/meme_4.8.0.tar.gz +# Download from eg. http://meme-suite.org/meme-software/4.8.0/meme_4.8.0.tar.gz sources = ['meme_%(version)s.tar.gz'] -source_urls = ['http://ebi.edu.au/ftp/software/MEME/%(version)s'] +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] dependencies = [ ('libxml2', '2.9.1'), -- GitLab From 764cddb8305556ed93969d90d2668708afb72fad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Jan 2017 15:04:13 +0100 Subject: [PATCH 158/818] adding easyconfigs: libconfig-1.5-intel-2016b.eb --- .../l/libconfig/libconfig-1.5-intel-2016b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.5-intel-2016b.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.5-intel-2016b.eb new file mode 100644 index 0000000000..8604d2ba03 --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.5-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.5' + +homepage = 'http://www.hyperrealm.com/libconfig/' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.hyperrealm.com/libconfig/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 26711df0d50150f06add6886d63b9c6761590c77 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 20 Jan 2017 10:03:21 +0800 Subject: [PATCH 159/818] also fix source urls for ghostscript versions 9.14 and 9.16 --- .../easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb index 97a129a9e5..907c72a138 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb @@ -10,7 +10,7 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} -source_urls = ["http://downloads.ghostscript.com/public/"] +source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 4e828aad87..16ce3919c6 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -10,7 +10,7 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True} -source_urls = ["http://downloads.ghostscript.com/public/"] +source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] checksums = ['829319325bbdb83f5c81379a8f86f38f'] diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb index 691a90006b..16b62cc65d 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} # lowopt (-O1) is used to avoid internal compiler error that is hit when -O2 is used toolchainopts = {'pic': True, 'lowopt': True} -source_urls = ["http://downloads.ghostscript.com/public/"] +source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] checksums = ['829319325bbdb83f5c81379a8f86f38f'] -- GitLab From fdbc7bb56e0eedfee2fac1d133bf1df997fbd4e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Jan 2017 11:27:03 +0100 Subject: [PATCH 160/818] adding easyconfigs: QuickFF-2.1.4-intel-2016b-Python-2.7.12.eb, yaff-1.0.develop.2.15-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb, molmod-1.1-intel-2016b-Python-2.7.12.eb --- .../molmod-1.1-intel-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ ...QuickFF-2.1.4-intel-2016b-Python-2.7.12.eb | 29 +++++++++++++++++ ...5-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb | 31 +++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QuickFF/QuickFF-2.1.4-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.15-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..23fd809bd7 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.1.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.1.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0de53d6790 --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.1.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'QuickFF' +version = '2.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/molmod/QuickFF/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), + ('molmod', '1.1', versionsuffix), + ('yaff', '1.0.develop.2.15', '%s-HDF5-1.8.18' % versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.15-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.15-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb new file mode 100644 index 0000000000..9f5b1ed999 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.15-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.0.develop.2.15' +hdf5ver = '1.8.18' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('h5py', '2.6.0', versionsuffix), + ('molmod', '1.1', '-Python-%(pyver)s'), +] + +options = {'modulename': name} +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'chem' -- GitLab From 74790fa8571999bbbe337bc7bc288a52161afc75 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 23 Jan 2017 11:48:31 +0800 Subject: [PATCH 161/818] remove hardcoded version --- easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index 582161abc9..95d35a2813 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -15,7 +15,7 @@ description = """The ChIP-Seq software provides methods for the analysis of ChIP toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/1.5.1/'] +source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/%s/' % '.'.join(version.split('-'))] sources = ['%(namelower)s.%(version)s.tar.gz'] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index 0bc8d276f9..5a91c1c288 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -15,7 +15,7 @@ description = """The ChIP-Seq software provides methods for the analysis of ChIP toolchain = {'name': 'goolf', 'version': '1.7.20'} -source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/1.5.1/'] +source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/%s/' % '.'.join(version.split('-'))] sources = ['%(namelower)s.%(version)s.tar.gz'] skipsteps = ['configure'] -- GitLab From 66eb83dcd0747ffd4790c59dd689a28c19abe5dc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 23 Jan 2017 18:18:38 +0800 Subject: [PATCH 162/818] add checksums --- .../easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb | 2 ++ .../easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb | 2 ++ .../easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb | 2 ++ .../easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb | 2 ++ .../easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb | 2 ++ .../easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb | 2 ++ easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 2 ++ .../easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb | 2 ++ .../easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb | 2 ++ easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb | 2 ++ easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb | 2 ++ easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb | 2 ++ 18 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb index 0e77075c8a..4562fea8de 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb @@ -13,6 +13,8 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] + # do not change the order of the patches or things will break patches = [ 'arpack-ng-3.1.3-update-to-head.patch', diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb index 8d3a7eb7fe..36abbfba39 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb @@ -12,6 +12,8 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] + # do not change the order of the patches or things will break patches = [ 'arpack-ng-3.1.3-update-to-head.patch', diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb index e75f54d2e1..a63af2d197 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb @@ -13,6 +13,8 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] + # do not change the order of the patches or things will break patches = [ 'arpack-ng-3.1.3-update-to-head.patch', diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb index ce27a87097..e390bd7768 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb @@ -12,6 +12,8 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] + # do not change the order of the patches or things will break patches = [ 'arpack-ng-3.1.3-update-to-head.patch', diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb index 0e9b24405d..b22908df9d 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb @@ -13,6 +13,8 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['d84e1b6108d9ee67c0d21aba7099e953'] + configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb index 6104f116d8..cdb3eae35c 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb @@ -12,6 +12,8 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['d84e1b6108d9ee67c0d21aba7099e953'] + configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index 95d35a2813..b0d7e2e41b 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/%s/' % '.'.join(version.split('-'))] sources = ['%(namelower)s.%(version)s.tar.gz'] +checksums = ['e36736c5151c872d9fc7afa54e3e8ccb'] + skipsteps = ['configure'] buildopts = ' CC=$CC' diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index 5a91c1c288..54bfcde59b 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['http://downloads.sourceforge.net/project/chip-seq/chip-seq/%s/' % '.'.join(version.split('-'))] sources = ['%(namelower)s.%(version)s.tar.gz'] +checksums = ['e36736c5151c872d9fc7afa54e3e8ccb'] + skipsteps = ['configure'] buildopts = ' CC=$CC' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb index 578d17b6ae..0e4a638848 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb @@ -13,6 +13,8 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f0c0a2670b08466a4050ddbd1f3de63'] + # expat, freetype and libpng are optional deps, # these are actually patched and included in the sources, dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb index 907c72a138..7d2dd7bf7c 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb @@ -13,6 +13,8 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] +checksums = ['024f040b1371348a2b7fc4d25b379d33'] + dependencies = [ ('freetype', '2.5.3'), ('fontconfig', '2.11.1'), diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb index 3347248cd1..7f241b6884 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb @@ -24,6 +24,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] +checksums = ['8e58583b4c2e1a1c661d271b94067e36'] + preconfigopts = "make configure && " dependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb index ce913425b7..316219216f 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb @@ -24,6 +24,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] +checksums = ['8e58583b4c2e1a1c661d271b94067e36'] + preconfigopts = "make configure && " dependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb index c516d9d10a..12ddedc547 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb @@ -25,6 +25,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] +checksums = ['f44e7c6c689f58d1876634aafe9fe1f9'] + preconfigopts = "make configure && " dependencies = [ diff --git a/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb index c9189d4325..343da7e2bc 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb @@ -24,6 +24,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] +checksums = ['099c655ce47361850fa07252497f64e7'] + preconfigopts = "make configure && " dependencies = [ diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb index 37e2c7a024..6d16b1a8fe 100644 --- a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-goolf-1.4.10.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://invisible-mirror.net/archives/lynx/tarballs/'] sources = ['%(name)s%(version)srel.2.tar.bz2'] +checksums = ['cb936aef812e4e463ab86cbbe14d4db9'] + sanity_check_paths = { 'files': ['bin/lynx'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb index 022bb67915..00b6eda668 100644 --- a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://invisible-mirror.net/archives/lynx/tarballs/'] sources = ['%(name)s%(version)srel.2.tar.bz2'] +checksums = ['cb936aef812e4e463ab86cbbe14d4db9'] + sanity_check_paths = { 'files': ['bin/lynx'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb index ab727c8b4c..2b1ca4f4f3 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb @@ -28,6 +28,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['meme_%(version)s.tar.gz'] source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +checksums = ['e1747a8a47a61d97256884c676b46c09'] + dependencies = [ ('libxml2', '2.9.1'), ('libxslt', '1.1.28'), diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb index c1658c0642..8c5d271d61 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb @@ -29,6 +29,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['meme_%(version)s.tar.gz'] source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +checksums = ['e1747a8a47a61d97256884c676b46c09'] + dependencies = [ ('libxml2', '2.9.1'), ('libxslt', '1.1.28'), -- GitLab From 5d5e297ac15a6802e7b6dfca44d2a5c3321f3275 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Mon, 23 Jan 2017 17:09:36 +0100 Subject: [PATCH 163/818] added conda-forge channel --- easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb index 401987f750..4b9209b380 100644 --- a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb +++ b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb @@ -15,7 +15,7 @@ description = """QIIME is an open-source bioinformatics pipeline for performing toolchain = {'name': 'dummy', 'version': ''} requirements = "%(namelower)s=%(version)s matplotlib=1.4.3 mock nose" -channels = ['bioconda'] +channels = ['bioconda', 'conda-forge'] builddependencies = [('Anaconda2', '4.2.0')] -- GitLab From 47623ed6c6f38360def694931573c1ee81abf14f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Jan 2017 14:00:53 +0100 Subject: [PATCH 164/818] fix ImageJ version (1.51i rather than 1.5.1i) --- .../i/ImageJ/{ImageJ-1.5.1i.eb => ImageJ-1.51i.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/ImageJ/{ImageJ-1.5.1i.eb => ImageJ-1.51i.eb} (88%) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb similarity index 88% rename from easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb rename to easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb index 1ae33a127b..8963988c6f 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.5.1i.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb @@ -1,7 +1,7 @@ easyblock = 'PackedBinary' name = 'ImageJ' -version = '1.5.1i' +version = '1.51i' homepage = 'https://imagej.nih.gov/ij' description = "Image Processing and Analysis in Java" @@ -9,7 +9,7 @@ description = "Image Processing and Analysis in Java" toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://imagej.nih.gov/ij/download/src/'] -sources = ['ij%s-src.zip' % ''.join(version.split('.'))] +sources = ['ij%(version_major)s%(version_minor)s-src.zip'] dependencies = [ ('Java', '1.8.0_112'), -- GitLab From 48eb10498a6fb04c50eec0c2d4be9a3fe0d20595 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Jan 2017 14:28:13 +0100 Subject: [PATCH 165/818] add FME extensions (+ deps) in R 3.3.1 easyconfigs --- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 4 ++++ easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 9e8837b860..7ed2007d87 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -466,6 +466,10 @@ exts_list = [ ('lubridate', '1.5.6', ext_options), ('biom', '0.3.12', ext_options), ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index ea4614f23d..e6d46c62ea 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -466,6 +466,10 @@ exts_list = [ ('lubridate', '1.5.6', ext_options), ('biom', '0.3.12', ext_options), ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index 21471e5985..09f5b0a4c6 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -466,6 +466,10 @@ exts_list = [ ('lubridate', '1.5.6', ext_options), ('biom', '0.3.12', ext_options), ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), ] moduleclass = 'lang' -- GitLab From 4a5d666df621d194775fdd4e321152b2b4c37713 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 25 Jan 2017 15:11:04 +0100 Subject: [PATCH 166/818] Beast v1.8.4 --- .../b/Beast/Beast-1.8.4-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb new file mode 100644 index 0000000000..cfdf71248e --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'Beast' +version = '1.8.4' + +homepage = 'http://beast.bio.ed.ac.uk/' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] +sources = ['BEASTv%(version)s.tgz'] + +dependencies = [ + ('Java', '1.8.0_74', '', ('dummy', '')), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 8de8facc59c1807a52f99264bcc24a4f8b5c1cf2 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 25 Jan 2017 15:25:16 +0100 Subject: [PATCH 167/818] toolchain for dependencies --- easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb index cfdf71248e..656a791b22 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb @@ -21,7 +21,7 @@ source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(vers sources = ['BEASTv%(version)s.tgz'] dependencies = [ - ('Java', '1.8.0_74', '', ('dummy', '')), + ('Java', '1.8.0_74', '', True), ] sanity_check_paths = { -- GitLab From 06f8e30bc932675f7091b408e87c41e0894f8255 Mon Sep 17 00:00:00 2001 From: Javier Antonio Ruiz Bosch Date: Wed, 25 Jan 2017 11:40:01 -0500 Subject: [PATCH 168/818] add cclib-1.5-foss-2016b-Python-3.2.5.eb easyconfig file --- .../cclib-1.5-foss-2016b-Python-3.5.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..78196b3b89 --- /dev/null +++ b/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'cclib' +version = '1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cclib.github.io/' +description = """cclib is a Python library that provides parsers for computational chemistry log files. + It alsoprovides a platform to implement algorithms in a package-independent manner. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/cclib/cclib/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.post1.tar.gz'] + +dependencies = [ + ('Python', '3.5.2'), # This contains numpy as extension needed for cclib +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' -- GitLab From 26bbcc867391a668ebd7d50390425e995e7515c3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 25 Jan 2017 23:54:33 +0100 Subject: [PATCH 169/818] adding easyconfigs: libgd-2.2.3-foss-2016b.eb --- .../l/libgd/libgd-2.2.3-foss-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100755 easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb new file mode 100755 index 0000000000..bfe540d4e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.3' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.12.1'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.26'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' -- GitLab From e3dcefcedfd21f97c0c09f1a88990185258d4fa4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 25 Jan 2017 23:58:41 +0100 Subject: [PATCH 170/818] adding easyconfigs: libcerf-1.4-foss-2016b.eb --- .../l/libcerf/libcerf-1.4-foss-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016b.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016b.eb new file mode 100644 index 0000000000..dd70dd1034 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.4' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From d693e82df07e1cc5750beb50a30e6f47d17bbcc6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 26 Jan 2017 00:02:29 +0100 Subject: [PATCH 171/818] adding easyconfigs: libcerf-1.5-foss-2016b.eb --- .../l/libcerf/libcerf-1.5-foss-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.5-foss-2016b.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-foss-2016b.eb new file mode 100644 index 0000000000..6a1a6a3a08 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.5' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 5e09e2ff0a6328e93e2efd7a714a0386e7e19a10 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 26 Jan 2017 18:12:03 +0100 Subject: [PATCH 172/818] 0.36 --- .../Trimmomatic-0.36-Java-1.8.0_92.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb new file mode 100644 index 0000000000..88a84647c6 --- /dev/null +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'Trimmomatic' +version = '0.36' + +homepage = 'http://www.usadellab.org/cms/?page=trimmomatic' +description = """Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data.The selection of trimming steps and their associated + parameters are supplied on the command line. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] +sources = [SOURCE_ZIP] + +java = 'Java' +javaver = '1.8.0_92' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute Trimmomatic run: java -jar \\$EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" + +sanity_check_paths = { + 'files': ["trimmomatic-%(version)s.jar"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From c9a2df738aff5a3a6985b9c428ed02ecbb772975 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 27 Jan 2017 09:01:43 +0100 Subject: [PATCH 173/818] Revert to libpng-1.6.24 --- easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb index bfe540d4e6..af1365b912 100755 --- a/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-foss-2016b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('fontconfig', '2.12.1'), ('libjpeg-turbo', '1.5.0'), - ('libpng', '1.6.26'), + ('libpng', '1.6.24'), ('zlib', '1.2.8'), ] -- GitLab From f2b5b86663eb4c0b35fbc26a7b09777aadacdbe4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 27 Jan 2017 11:39:18 +0100 Subject: [PATCH 174/818] changed msg --- .../easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb index 88a84647c6..4ddd5946b8 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb @@ -18,7 +18,7 @@ javaver = '1.8.0_92' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute Trimmomatic run: java -jar \\$EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" +modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" sanity_check_paths = { 'files': ["trimmomatic-%(version)s.jar"], -- GitLab From 6f4e932daa5902853c5fc3bb475bbe2d17d80099 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 27 Jan 2017 11:54:30 +0100 Subject: [PATCH 175/818] use dummy toolchain, rename eb --- .../b/Beast/{Beast-1.8.4-foss-2016a.eb => Beast-1.8.4.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/b/Beast/{Beast-1.8.4-foss-2016a.eb => Beast-1.8.4.eb} (95%) diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb similarity index 95% rename from easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb rename to easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 656a791b22..972161d135 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -16,7 +16,8 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. """ -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'dummy', 'version': ''} + source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] sources = ['BEASTv%(version)s.tgz'] -- GitLab From c41a28090f6bfb672ed832bdbfe58660e1372fe4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 30 Jan 2017 16:31:50 +0100 Subject: [PATCH 176/818] adding easyconfigs: libxslt-1.1.29-foss-2016b.eb --- .../l/libxslt/libxslt-1.1.29-foss-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-foss-2016b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-foss-2016b.eb new file mode 100644 index 0000000000..42e7a06480 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.29' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.4'), +] + +moduleclass = 'lib' -- GitLab From cda6e2019665e299eb669b7fca6cd4e5e0ee9b1e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 30 Jan 2017 18:38:28 +0100 Subject: [PATCH 177/818] adding easyconfigs: Pindel-0.2.5b8-foss-2016b.eb --- .../p/Pindel/Pindel-0.2.5b8-foss-2016b.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb new file mode 100644 index 0000000000..9f45199e95 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 0.2.5b8 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CmdCp' + +name = 'Pindel' +version = '0.2.5b8' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/genome/pindel/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['pindel-perl-path.patch'] + +dependencies = [ + ('HTSlib', '1.3.1'), + ('zlib', '1.2.8') +] + +cmds_map = [('.*', "CPATH=$EBROOTHTSLIB/include/bam:$CPATH ./INSTALL $EBROOTHTSLIB")] + +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" +] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 37fb1386845e8df3ec15f2da48bb898d549d1e02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Jan 2017 19:16:15 +0100 Subject: [PATCH 178/818] adding easyconfigs: Inspector-2017_update1.eb --- .../i/Inspector/Inspector-2017_update1.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb new file mode 100644 index 0000000000..5e1233098f --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb @@ -0,0 +1,16 @@ +name = 'Inspector' +version = '2017_update1' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_%(version)s.tar.gz'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From 994c8c8af07bed10290e1dfef70c44be553147e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Jan 2017 19:26:33 +0100 Subject: [PATCH 179/818] adding easyconfigs: NEURON-7.4-intel-2016b.eb --- .../n/NEURON/NEURON-7.4-intel-2016b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEURON/NEURON-7.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/n/NEURON/NEURON-7.4-intel-2016b.eb b/easybuild/easyconfigs/n/NEURON/NEURON-7.4-intel-2016b.eb new file mode 100644 index 0000000000..0a3e0085b0 --- /dev/null +++ b/easybuild/easyconfigs/n/NEURON/NEURON-7.4-intel-2016b.eb @@ -0,0 +1,18 @@ +name = 'NEURON' +version = '7.4' + +homepage = 'http://www.neuron.yale.edu/neuron' +description = """Empirically-based simulations of neurons and networks of neurons.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['nrn-%(version)s.tar.gz'] +source_urls = ['http://www.neuron.yale.edu/ftp/neuron/versions/v%(version)s/'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('Python', '2.7.12') +] + +moduleclass = 'math' -- GitLab From 5cfe6a3c3c4afe184f697af9644c71e8356ff912 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 08:49:14 +0100 Subject: [PATCH 180/818] adding easyconfigs: Molden-5.7-intel-2016b.eb --- .../m/Molden/Molden-5.7-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb b/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb new file mode 100644 index 0000000000..72b0830332 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '5.7' + +homepage = 'http://www.cmbi.ru.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(namelower)s%(version)s.tar.gz'] +source_urls = ['ftp://ftp.cmbi.ru.nl/pub/molgraph/molden'] + +buildopts = 'CC="$CC" FC="$F90" molden' + +files_to_copy = [(['molden'], 'bin'), 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/molden', 'README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From cb17c3afce0ad722234cf1d460bac0e6f238e66c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 09:28:32 +0100 Subject: [PATCH 181/818] include X11 as dep for Molden --- easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb b/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb index 72b0830332..fe23519684 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = ['%(namelower)s%(version)s.tar.gz'] source_urls = ['ftp://ftp.cmbi.ru.nl/pub/molgraph/molden'] +dependencies = [('X11', '20160819')] + buildopts = 'CC="$CC" FC="$F90" molden' files_to_copy = [(['molden'], 'bin'), 'CopyRight', 'README', 'REGISTER'] -- GitLab From e80220d61a80333c467f1b8d7f6b96a7f73f1f94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 09:51:45 +0100 Subject: [PATCH 182/818] remove incorrect definition for $ROSETTA_DB, now (correctly) defined via Rosetta easyblock --- .../r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb | 4 ---- .../easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb | 4 ---- easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb | 4 ---- 3 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb index 10b2a8fd9c..64d1ea29a2 100644 --- a/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb @@ -13,8 +13,4 @@ sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] -modextravars = { - 'ROSETTA3_DB': '$root/database', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb index 86250d9275..d65a2614d9 100644 --- a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb @@ -13,8 +13,4 @@ sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] builddependencies = [('SCons', '2.4.1', '-Python-2.7.11')] -modextravars = { - 'ROSETTA3_DB': '$root/database', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb index dc1928028e..00858b739e 100644 --- a/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb @@ -13,8 +13,4 @@ sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] builddependencies = [('SCons', '2.5.0', '-Python-2.7.12')] -modextravars = { - 'ROSETTA3_DB': '$root/database', -} - moduleclass = 'bio' -- GitLab From 83154d12a7f3621cb005097bfed152a0e9efb47f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 13:42:21 +0100 Subject: [PATCH 183/818] adding easyconfigs: Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb --- ...f-python-3.2.0-intel-2016b-Python-3.5.2.eb | 29 +++++++++++++++ .../p/protobuf/protobuf-3.2.0-intel-2016b.eb | 21 +++++++++++ ...sorflow-0.12.1-intel-2016b-Python-3.5.2.eb | 35 +++++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..89a06c0e60 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.2.0' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb new file mode 100644 index 0000000000..087e4b2fe4 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.2.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +preconfigopts = "./autogen.sh &&" + +sanity_check_paths = { + 'files': ['bin/protoc','lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..4898d79427 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '3' +pymin = '5' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/e5/5c/56e6522fdcd6f8739dcbc4de62e8b0040e141785bb42e5b53a83b0ba3e58/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['c6e3ba8579754f37d37be26e863f9d95'] + +dependencies = [ + ('Python', '%s.%s.2' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 9d56a6afba449a92eec678b117e30cd9eff5e28f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 14:01:30 +0100 Subject: [PATCH 184/818] adding easyconfigs: Rosetta-2016.46.59086-foss-2016b.eb --- .../Rosetta/Rosetta-2016.46.59086-foss-2016b.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-2016.46.59086-foss-2016b.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.46.59086-foss-2016b.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.46.59086-foss-2016b.eb new file mode 100644 index 0000000000..ccf154c6cb --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.46.59086-foss-2016b.eb @@ -0,0 +1,16 @@ +name = 'Rosetta' +version = '2016.46.59086' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.5.0', '-Python-2.7.12')] + +moduleclass = 'bio' -- GitLab From 4c5c0258aecc0af48800143ea9f3d52d0155fb75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 14:44:17 +0100 Subject: [PATCH 185/818] add Autotools build dep for protobuf --- .../easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb | 6 ++++-- .../easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb index 14ba425f1f..d684c53f55 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb @@ -11,10 +11,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] sources = [SOURCE_TAR_GZ] -preconfigopts = "./autogen.sh &&" +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " sanity_check_paths = { - 'files': ['bin/protoc','lib/libprotobuf.%s' % SHLIB_EXT], + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb index 087e4b2fe4..224169f86e 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-2016b.eb @@ -11,10 +11,12 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] sources = [SOURCE_TAR_GZ] -preconfigopts = "./autogen.sh &&" +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " sanity_check_paths = { - 'files': ['bin/protoc','lib/libprotobuf.%s' % SHLIB_EXT], + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 7fb56afbc203e5b3ed0f29102e87d27c4861df87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2017 14:46:10 +0100 Subject: [PATCH 186/818] adding easyconfigs: FLUENT-18.0.eb --- easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb new file mode 100644 index 0000000000..7feeec83d4 --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb @@ -0,0 +1,14 @@ +name = 'FLUENT' +version = '18.0' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDSTRUCTURES_%(version_major)s%(version_minor)s_LINX64.tar'] + +moduleclass = 'cae' -- GitLab From a00bf1bd323e4043a72c4c33631adf178f2e42a1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 31 Jan 2017 18:18:19 +0100 Subject: [PATCH 187/818] adding easyconfigs: matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb --- ...atplotlib-1.5.3-foss-2016b-Python-3.5.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100755 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..fd17adf8c2 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('freetype', '2.7'), + ('libpng', '1.6.26'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 853f93e9c355e468cd204c175292711ca6051aa4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 31 Jan 2017 18:19:51 +0100 Subject: [PATCH 188/818] adding easyconfigs: scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb, scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb, scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb, scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb --- ...t-learn-0.18.1-foss-2016b-Python-2.7.12.eb | 30 +++++++++++++++++++ ...it-learn-0.18.1-foss-2016b-Python-3.5.2.eb | 30 +++++++++++++++++++ ...-learn-0.18.1-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++++++++ ...t-learn-0.18.1-intel-2016b-Python-3.5.2.eb | 30 +++++++++++++++++++ 4 files changed, 120 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..9e8395819b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..dd9bbeb576 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('matplotlib', '1.5.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..ad5177d70b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..8d85cb18f4 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('matplotlib', '1.5.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 8481b1ae480bb16ac01b91bd53915f454c96c57c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Feb 2017 11:40:59 +0100 Subject: [PATCH 189/818] bumo to final OpenMPI 2.0.2 --- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 1676fb43ff..2e2eda32d4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -sources = ['openmpi-%(version)src2.tar.gz'] # FIXME +sources = ['openmpi-%(version)s.tar.gz'] +checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -- GitLab From 56782c46c4046221e6c09b9d73d91a592b3e6c72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Feb 2017 11:47:19 +0100 Subject: [PATCH 190/818] bump to FFTW 3.3.6 --- .../{FFTW-3.3.5-gompi-2017a.eb => FFTW-3.3.6-gompi-2017a.eb} | 5 +++-- easybuild/easyconfigs/f/foss/foss-2017a.eb | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.5-gompi-2017a.eb => FFTW-3.3.6-gompi-2017a.eb} (78%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb similarity index 78% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 66f9239e19..039c1bb824 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -1,5 +1,5 @@ name = 'FFTW' -version = '3.3.5' +version = '3.3.6' homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) @@ -8,8 +8,9 @@ description = """FFTW is a C subroutine library for computing the discrete Fouri toolchain = {'name': 'gompi', 'version': '2017a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] runtest = 'check' diff --git a/easybuild/easyconfigs/f/foss/foss-2017a.eb b/easybuild/easyconfigs/f/foss/foss-2017a.eb index badece0d08..400c0029a9 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017a.eb @@ -28,7 +28,7 @@ dependencies = [ ('GCC', gccver), ('OpenMPI', '2.0.2', '', ('GCC', gccver)), (blaslib, blasver, blassuff, ('GCC', gccver)), - ('FFTW', '3.3.5', '', comp_mpi_tc), + ('FFTW', '3.3.6', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] -- GitLab From ec7e97a48bbe83f3b1d777628bd0f1d4966dfb99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Feb 2017 11:55:33 +0100 Subject: [PATCH 191/818] bump copyright to 2017 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 3979a91f64..350d5c333c 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2016 Ghent University +# Copyright 2012-2017 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -- GitLab From a9e7d44acaa0d98b7ff80dcc16fc8aa596dbd6f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Feb 2017 14:36:33 +0100 Subject: [PATCH 192/818] also install intel-gdb components in icc/ifort easyconfigs --- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index 4b07bc6dde..39745a0399 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -24,7 +24,7 @@ dependencies = [ # list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide -components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] dontcreateinstalldir = 'True' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index 4c71563eb3..746cfd78bf 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -27,7 +27,7 @@ dependencies = [ # list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide -components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] dontcreateinstalldir = 'True' -- GitLab From 4e1ad10fd35f1f4fb5d98d5f33e6c049e7959738 Mon Sep 17 00:00:00 2001 From: hpcswadm Date: Wed, 1 Feb 2017 11:25:15 -0500 Subject: [PATCH 193/818] adding easyconfigs: ipp-2017.1.132.eb --- easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb diff --git a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb new file mode 100644 index 0000000000..0e78bfb109 --- /dev/null +++ b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb @@ -0,0 +1,19 @@ +name = 'ipp' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/articles/intel-ipp/' +description = """Intel Integrated Performance Primitives (Intel IPP) is an extensive library + of multicore-ready, highly optimized software functions for multimedia, data processing, + and communications applications. Intel IPP offers thousands of optimized functions + covering frequently used fundamental algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ipp_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'perf' -- GitLab From e5abb209ec4f358b6b75a80543c854d33207274c Mon Sep 17 00:00:00 2001 From: hpcswadm Date: Wed, 1 Feb 2017 11:33:28 -0500 Subject: [PATCH 194/818] adding easyconfigs: tbb-2017.2.132.eb --- easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb new file mode 100644 index 0000000000..c81d846fca --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb @@ -0,0 +1,22 @@ +name = 'tbb' +version = '2017.2.132' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +description = """Intel Threading Building Blocks 4.0 (Intel TBB) + is a widely used, award-winning C++ template library for creating reliable, + portable, and scalable parallel applications. + Use Intel TBB for a simple and rapid way of developing robust task-based + parallel applications that scale to available processor cores, are compatible + with multiple environments, and are easier to maintain. + Intel TBB is the most proficient way to implement future-proof parallel applications + that tap into the power and performance of multicore and manycore hardware platforms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_%(name)s_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'lib' -- GitLab From 55b2a4d6c41f07d82a221aa26496acece19035b4 Mon Sep 17 00:00:00 2001 From: hpcswadm Date: Wed, 1 Feb 2017 11:36:26 -0500 Subject: [PATCH 195/818] adding easyconfigs: itac-2017.1.024.eb --- .../easyconfigs/i/itac/itac-2017.1.024.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2017.1.024.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb new file mode 100644 index 0000000000..f4c7fa5a53 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb @@ -0,0 +1,20 @@ +name = 'itac' +version = '2017.1.024' + +homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_itac_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +preferredmpi = 'impi5' + +# license file +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From b96a076e60218148fe73b2beb89a2bd5bbf17eab Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 2 Feb 2017 11:34:38 +0800 Subject: [PATCH 196/818] fix checksum --- .../easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb index 7d2dd7bf7c..9bdfb72977 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/old-gs-releases/"] sources = [SOURCELOWER_TAR_GZ] -checksums = ['024f040b1371348a2b7fc4d25b379d33'] +checksums = ['586494befb443363338c1b6379f13973'] dependencies = [ ('freetype', '2.5.3'), -- GitLab From c505725c9c47e141934a0717c3172bcbae5df428 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Feb 2017 15:33:10 +0100 Subject: [PATCH 197/818] adding easyconfigs: statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb --- ...tsmodels-0.6.1-intel-2016b-Python-3.5.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..435f33a3bd --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'statsmodels' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://statsmodels.sourceforge.net/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '3.5.2')] + +exts_list = [ + ('patsy', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'source_tmpl': 'patsy-%(version)s.zip', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/sources/statsmodels'], + 'source_tmpl': 'statsmodels-%(version)s.zip', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' -- GitLab From 6f5b48e3b6be222884ce59fb87e880b594b3500f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 2 Feb 2017 17:24:20 +0100 Subject: [PATCH 198/818] adding easyconfigs: PyTables-3.2.2-foss-2016b-Python-2.7.12.eb, numexpr-2.6.1-foss-2016b-Python-2.7.12.eb --- .../numexpr-2.6.1-foss-2016b-Python-2.7.12.eb | 27 +++++++++++++ ...PyTables-3.2.2-foss-2016b-Python-2.7.12.eb | 38 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1cddd58e1d --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..836640b941 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v.%(version)s.tar.gz'] + +patches = ['pyTables-%(version)s-fix-libs.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('numpy', '1.11.1', versionsuffix), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.17'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' -- GitLab From 0c636d19ee317d5fa00c83d351550ef292f91e44 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 2 Feb 2017 18:27:07 +0100 Subject: [PATCH 199/818] adding easyconfigs: Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb, protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb --- ...-python-3.2.0-intel-2016b-Python-2.7.12.eb | 29 +++++++++++++++ ...orflow-0.12.1-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100755 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..136b95fa55 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.2.0' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..8ccd735bee --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/7e/c6/837f4e249aae5c86a632eaaa9779e601eca1487772f8ad75c347bf9e813f/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['c98fd26b79a97cc490c942bbafed5462'] + +dependencies = [ + ('Python', '%s.%s.12' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From f0732795647bda8bbd383479e74f6110f557a889 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 3 Feb 2017 17:07:14 +0800 Subject: [PATCH 200/818] prepare release notes for eb310 --- RELEASE_NOTES | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 3ed16807e4..c5b786547f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,44 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,225 easyconfig files, for 1,136 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.0 (February 3rd 2017) +-------------------------- + +feature release +- added example easyconfig files for 16 new software packages: + - ack (#3983), cclib (#4065), ConnectomeWorkbench (#3411), GroIMP (#3994), hyperspy (#3991), I-TASSER (#1216), ImageJ (#4023), + libconfig (#4051), libspatialindex (#4002), mahotas (#3990), Minia (#3949), muParser (#4007), NetLogo (#3941), QIIME (#3868), + QwtPolar (#4019), Tensorflow (#4084, #4095) +- added additional easyconfigs for various supported software packages: + - ALPS 2.3.0 (#4021), Anaconda2 and Anaconda3 4.2.0 (#4005), bbcp 12.01.30.00.0 (#4026), Beast 1.8.4 (#4064), + Boost 1.62.0 (#3650) and 1.63.0 (#3977), CD-HIT 4.6.6 (#3995), CP2K 4.1 (#3890), EIGENSORT 6.1.4 (#3962), ELPA 2016.05.004 (#3999), + EMBOSS 6.6.0 (#3980), FLUENT 18.0 (#4086), GATK 3.7 (#4017), GDAL 2.1.2 (#4015), GSL 2.3 (#3961), HPL 2.2 (#3968, #3969), Inspector 2017_update1 (#4079), + ipp 2017.1.132 (#4090), itac 2017.1.024 (#4092), Kraken 0.10.5-beta (#3963), libcerf 1.4 (#4067) and 1.5 (#4068), libevent 2.0.22 (#4014), + libgd 2.2.3 (#4066), libharu 2.3.0 (#3980), libpciaccess 0.13.4 (#4031), libpthread-stubs 0.3 (#4029, #4034), libspatialindex 1.8.5 (#4016), + libxslt 1.1.29 (#4077), libxsmm 1.6.4 (#3890), matplotlib 1.4.3 (#3998) and 1.5.3 (#4087), Molden 5.7 (#4081), molmod 1.1 (#4053), netCDF 4.4.1.1 (#4000), + NEURON 7.4 (#4080), OpenSSL 1.1.0c (#4047), PEAR 0.9.8 (#3992), Perl 5.24.0 (#4047), Pindel 0.2.5b8 (#4078), PLUMED 2.3.0 (#3989), protobuf 2.5.0 (#4027), + Python 3.5.1 (#3981), PyQt5 5.7.1 and PyQt 4.12 (#4018), QCA 2.1.0 (#4020), Qt5 5.7.1 (#4001), QuickFF 2.1.4 (#4053), rhdf5 2.18.0 (#3982), Rosetta 2016.46.59086 (#4085), + scikit-learn 0.18.1 (#4088), SIP 4.19 (#4018), statsmodels 0.6.1 (#4093), tbb 2017.2.132 (#4091), tmux 2.3 (#4014), Trimmomatic 0.36 (#4070), WPS 3.8 and WRF 3.8 (#3970), + X11 20160819 (#3981), Xerces-C++ 3.1.3 (#4008), xorg-macros 1.19.0 (#4030), yaff 1.0.develop.2.15 (#4053), Yase 2016.06a (#3987), zlib 1.2.10 (#3967) +- various enhancements, including: + - update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests (#3985) + - adding channel to perl-app-cpanminus (#4012) + - add FME extensions (+ deps) in R 3.3.1 easyconfigs (#4063) +- various bug fixes, including: + - add libxml2 dependency on HDF5 (#3759) + - remove unnecessary dependency in libmatheval (#3988) + - fix permissions on SWASH binaries (#4003) + - add missing deps (libpthread-stubs, libpciaccess) to libdrm 2.4.70 (#4032) + - modloadmsg style fixes in multiple easyconfigs (#4035) + - fix ImageJ version (1.51i rather than 1.5.1i) (#4062) + - include X11 as dep for Molden (#4082) + - remove incorrect definition for $ROSETTA3_DB, now (correctly) defined via Rosetta easyblock (#4083) +- fix source URLs for several easyconfigs, including: + - arpack-ng 3.1.3 and 3.1.5, ChIP-Seq 1.5-1, Ghostscript 9.10, 9.14 and 9.16, Git 1.7.12, 1.8.2 and 1.8.3.1, lynx 2.8.7 and MEME 4.8.0 (#4050), + HBase 1.0.2 (#4043), libevent 2.0.22 (#4037), libsodium 1.0.3 (#4046), Maven 3.2.2 and 3.3.3 (#4039), PCC 20131024 (#4044), S-Lang 2.3.0 (#4045), + Spark 1.3.0 (#4041), splitRef 0.0.2 (#4040), zlib 1.2.10 (#4042) + + v3.0.2 (December 22nd 2016) --------------------------- -- GitLab From 4be7ad85dfef8ab868ea0b4d8ba579d3bde5b267 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Feb 2017 10:54:45 +0100 Subject: [PATCH 201/818] complete easybuild-easyconfigs v3.1.0 release notes & bump version --- RELEASE_NOTES | 31 +++++++++++-------------------- setup.py | 2 +- 2 files changed, 12 insertions(+), 21 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c5b786547f..a293eb1659 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,225 easyconfig files, for 1,136 different software packages, +The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.1.0 (February 3rd 2017) @@ -11,37 +11,28 @@ v3.1.0 (February 3rd 2017) feature release - added example easyconfig files for 16 new software packages: - - ack (#3983), cclib (#4065), ConnectomeWorkbench (#3411), GroIMP (#3994), hyperspy (#3991), I-TASSER (#1216), ImageJ (#4023), - libconfig (#4051), libspatialindex (#4002), mahotas (#3990), Minia (#3949), muParser (#4007), NetLogo (#3941), QIIME (#3868), - QwtPolar (#4019), Tensorflow (#4084, #4095) -- added additional easyconfigs for various supported software packages: - - ALPS 2.3.0 (#4021), Anaconda2 and Anaconda3 4.2.0 (#4005), bbcp 12.01.30.00.0 (#4026), Beast 1.8.4 (#4064), - Boost 1.62.0 (#3650) and 1.63.0 (#3977), CD-HIT 4.6.6 (#3995), CP2K 4.1 (#3890), EIGENSORT 6.1.4 (#3962), ELPA 2016.05.004 (#3999), - EMBOSS 6.6.0 (#3980), FLUENT 18.0 (#4086), GATK 3.7 (#4017), GDAL 2.1.2 (#4015), GSL 2.3 (#3961), HPL 2.2 (#3968, #3969), Inspector 2017_update1 (#4079), - ipp 2017.1.132 (#4090), itac 2017.1.024 (#4092), Kraken 0.10.5-beta (#3963), libcerf 1.4 (#4067) and 1.5 (#4068), libevent 2.0.22 (#4014), - libgd 2.2.3 (#4066), libharu 2.3.0 (#3980), libpciaccess 0.13.4 (#4031), libpthread-stubs 0.3 (#4029, #4034), libspatialindex 1.8.5 (#4016), - libxslt 1.1.29 (#4077), libxsmm 1.6.4 (#3890), matplotlib 1.4.3 (#3998) and 1.5.3 (#4087), Molden 5.7 (#4081), molmod 1.1 (#4053), netCDF 4.4.1.1 (#4000), - NEURON 7.4 (#4080), OpenSSL 1.1.0c (#4047), PEAR 0.9.8 (#3992), Perl 5.24.0 (#4047), Pindel 0.2.5b8 (#4078), PLUMED 2.3.0 (#3989), protobuf 2.5.0 (#4027), - Python 3.5.1 (#3981), PyQt5 5.7.1 and PyQt 4.12 (#4018), QCA 2.1.0 (#4020), Qt5 5.7.1 (#4001), QuickFF 2.1.4 (#4053), rhdf5 2.18.0 (#3982), Rosetta 2016.46.59086 (#4085), - scikit-learn 0.18.1 (#4088), SIP 4.19 (#4018), statsmodels 0.6.1 (#4093), tbb 2017.2.132 (#4091), tmux 2.3 (#4014), Trimmomatic 0.36 (#4070), WPS 3.8 and WRF 3.8 (#3970), - X11 20160819 (#3981), Xerces-C++ 3.1.3 (#4008), xorg-macros 1.19.0 (#4030), yaff 1.0.develop.2.15 (#4053), Yase 2016.06a (#3987), zlib 1.2.10 (#3967) + - ack (#3983), cclib (#4065), ConnectomeWorkbench (#3411), GroIMP (#3994), hyperspy (#3991), I-TASSER (#1216), + ImageJ (#4023, #4062), libconfig (#4051), libspatialindex (#4002), mahotas (#3990), Minia (#3949), muParser (#4007), + NetLogo (#3941), QIIME (#3868), QwtPolar (#4019), Tensorflow (#4084, #4095) +- added additional easyconfigs for various supported software packages, including: + - Boost 1.62.0 + 1.63.0, CP2K 4.1, GSL 2.3, PLUMED 2.3.0, Qt5 5.7.1, WRF 3.8, WPS 3.8, Yade 2016.06a, zlib 1.2.11 - various enhancements, including: - update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests (#3985) - - adding channel to perl-app-cpanminus (#4012) - add FME extensions (+ deps) in R 3.3.1 easyconfigs (#4063) - various bug fixes, including: - add libxml2 dependency on HDF5 (#3759) - remove unnecessary dependency in libmatheval (#3988) - fix permissions on SWASH binaries (#4003) + - add conda-forge channel to perl-app-cpanminus (#4012) - add missing deps (libpthread-stubs, libpciaccess) to libdrm 2.4.70 (#4032) - modloadmsg style fixes in multiple easyconfigs (#4035) - - fix ImageJ version (1.51i rather than 1.5.1i) (#4062) - include X11 as dep for Molden (#4082) - remove incorrect definition for $ROSETTA3_DB, now (correctly) defined via Rosetta easyblock (#4083) - fix source URLs for several easyconfigs, including: - - arpack-ng 3.1.3 and 3.1.5, ChIP-Seq 1.5-1, Ghostscript 9.10, 9.14 and 9.16, Git 1.7.12, 1.8.2 and 1.8.3.1, lynx 2.8.7 and MEME 4.8.0 (#4050), - HBase 1.0.2 (#4043), libevent 2.0.22 (#4037), libsodium 1.0.3 (#4046), Maven 3.2.2 and 3.3.3 (#4039), PCC 20131024 (#4044), S-Lang 2.3.0 (#4045), - Spark 1.3.0 (#4041), splitRef 0.0.2 (#4040), zlib 1.2.10 (#4042) + - arpack-ng 3.1.3 + 3.1.5 (#4050), ChIP-Seq 1.5-1 (#4050), Ghostscript 9.10, 9.14 + 9.16 (#4050), + Git 1.7.12, 1.8.2 + 1.8.3.1 (#4050), HBase 1.0.2 (#4043), libevent 2.0.22 (#4037), libsodium 1.0.3 (#4046), + lynx 2.8.7 (#4050), Maven 3.2.2 and 3.3.3 (#4039), MEME 4.8.0 (#4050), PCC 20131024 (#4044), S-Lang 2.3.0 (#4045), + Spark 1.3.0 (#4041), splitRef 0.0.2 (#4040) v3.0.2 (December 22nd 2016) diff --git a/setup.py b/setup.py index 350d5c333c..a3f5efb8ac 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.0.2' +VERSION = '3.1.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 56d9163978843a201930d0e1feeca6b337013a14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Feb 2017 11:16:30 +0100 Subject: [PATCH 202/818] also mention foss/2017a and intel/2017a in EB v3.1.0 release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a293eb1659..a240d6d9d8 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -10,6 +10,7 @@ v3.1.0 (February 3rd 2017) -------------------------- feature release +- added easyconfigs for foss/2017a and intel/2017a common toolchains (#3968, #3969) - added example easyconfig files for 16 new software packages: - ack (#3983), cclib (#4065), ConnectomeWorkbench (#3411), GroIMP (#3994), hyperspy (#3991), I-TASSER (#1216), ImageJ (#4023, #4062), libconfig (#4051), libspatialindex (#4002), mahotas (#3990), Minia (#3949), muParser (#4007), -- GitLab From 5fcb829872dfb476fdd3c7fc0a2ef897b43a65bc Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 2 Feb 2017 14:53:34 +0000 Subject: [PATCH 203/818] Added MCR 2013b, 2014b, 2015b, 2016b with Java 1.8.0_121 as dependency --- easybuild/easyconfigs/m/MCR/MCR-R2013b.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2014b.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2015b.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2016b.eb | 18 ++++++++++++++++++ 4 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2013b.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2014b.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2015b.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2016b.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb new file mode 100644 index 0000000000..ea139590d9 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2013b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb new file mode 100644 index 0000000000..1aaf919350 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2014b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb new file mode 100644 index 0000000000..02cf05532e --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2015b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb new file mode 100644 index 0000000000..78ab492fb8 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2016b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' -- GitLab From 2247e3141717a397e142124699e715c75eb94f4d Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 2 Feb 2017 14:16:51 +0000 Subject: [PATCH 204/818] Added Java 1.8.0_121, which is the latest version --- easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb new file mode 100644 index 0000000000..f95da7cf07 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_121' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 4fedf3d3a72e444fc495475e8902d5fce325e111 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Feb 2017 15:29:18 +0100 Subject: [PATCH 205/818] adding easyconfigs: EasyBuild-3.1.0.eb --- .../e/EasyBuild/EasyBuild-3.1.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb new file mode 100644 index 0000000000..606f9a318d --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/94/54/611cb71c61aae9833ee87e7d86768e9a86b411afe9f608c15e267fe7a986', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/fd/dd/83d8ef6a981c9e953f523328d5fba23b1be84fb7640a2c1d8b8e66b07102', + # easybuild-easyblocks + 'https://pypi.python.org/packages/73/0f/4681ae27ac06deac1225efc807f02c2305259e6b60e6037716a3f2f327d3', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/fa/4c/a83e7d70564c883e6a23cfcb4e0e4fea94da0947cc970652eda63f9f9765', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.22.tar.gz', + 'vsc-base-2.5.7.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From bfecb9916c49d2f19d942dcb4d5a9d6153fac0ba Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Fri, 3 Feb 2017 16:40:02 +0000 Subject: [PATCH 206/818] Allow intel 2017 to compile --- .../b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb | 20 +++++++++++++++++++ easybuild/easyconfigs/b/Bowtie/void2int.patch | 13 ++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb create mode 100644 easybuild/easyconfigs/b/Bowtie/void2int.patch diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb new file mode 100644 index 0000000000..500679eb6f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb @@ -0,0 +1,20 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'iimkl', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['int64typedef.patch','void2int.patch'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/void2int.patch b/easybuild/easyconfigs/b/Bowtie/void2int.patch new file mode 100644 index 0000000000..80b76591d4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/void2int.patch @@ -0,0 +1,13 @@ +--- processor_support.h.orig 2017-02-02 21:48:42.436432756 +0000 ++++ processor_support.h 2017-02-02 21:48:54.419309743 +0000 +@@ -44,8 +44,8 @@ + + try { + #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) +- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception +- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX ++ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception ++ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else -- GitLab From cfcada98291a92ba8989119892999eb990644080 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 5 Feb 2017 23:04:31 +0100 Subject: [PATCH 207/818] adding easyconfigs: Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb, arpack-ng-3.4.0-foss-2016b.eb --- ...adillo-7.600.2-foss-2016b-Python-2.7.12.eb | 23 +++++++++++++++++ .../a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb | 25 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8f548fef7d --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Armadillo' +version = '7.600.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://sourceforge.net/projects/arma/files'] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('arpack-ng', '3.4.0'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.2')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb new file mode 100644 index 0000000000..9320f188ec --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From eddb755218b40bd824e560f71a8579c0316a8fc7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 5 Feb 2017 23:46:40 +0100 Subject: [PATCH 208/818] adding easyconfigs: protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb, protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb, protobuf-3.2.0-foss-2016b.eb, Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb, Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb --- ...f-python-3.2.0-foss-2016b-Python-2.7.12.eb | 29 +++++++++++++++ ...uf-python-3.2.0-foss-2016b-Python-3.5.2.eb | 29 +++++++++++++++ .../p/protobuf/protobuf-3.2.0-foss-2016b.eb | 23 ++++++++++++ ...sorflow-0.12.1-foss-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ ...nsorflow-0.12.1-foss-2016b-Python-3.5.2.eb | 35 +++++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb create mode 100755 easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..25a3d48ede --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.2.0' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..a88f02f65a --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.2.0' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb new file mode 100755 index 0000000000..f6b756484f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.2.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..b94ca618c9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2016b'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/7e/c6/837f4e249aae5c86a632eaaa9779e601eca1487772f8ad75c347bf9e813f/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['c98fd26b79a97cc490c942bbafed5462'] + +dependencies = [ + ('Python', '%s.%s.12' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..d8b2947422 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2016b'} + +pymaj = '3' +pymin = '5' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/e5/5c/56e6522fdcd6f8739dcbc4de62e8b0040e141785bb42e5b53a83b0ba3e58/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['c6e3ba8579754f37d37be26e863f9d95'] + +dependencies = [ + ('Python', '%s.%s.2' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 92797f67325c275d17e41b0927a882b744761024 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 6 Feb 2017 10:29:09 +0100 Subject: [PATCH 209/818] adding easyconfigs: DIAMOND-0.8.35-goolf-1.7.20.eb --- .../d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb new file mode 100644 index 0000000000..19f96d592f --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'DIAMOND' +version = '0.8.35' + +homepage = 'https://github.com/bbuchfink/diamond' +description = """Accelerated BLAST compatible local sequence aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/bbuchfink/diamond/archive/'] +sources = ['v%(version)s.tar.gz'] + +separate_build_dir = True + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/diamond'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 511de25f91be78fdd24e8e7fe913e3b4dce1c4c6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 8 Feb 2017 13:41:32 +0100 Subject: [PATCH 210/818] Add patch to work around build failures with GCC 6 --- .../pkg-config-0.29.1-foss-2017a.eb | 30 +++++++++++++++++++ .../pkg-config/pkg-config-0.29.1_gcc-6.patch | 22 ++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb new file mode 100644 index 0000000000..b3ddd790cb --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +patches = [ + 'pkg-config-%(version)s_gcc-6.patch', +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch new file mode 100644 index 0000000000..a83002f30d --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch @@ -0,0 +1,22 @@ +Work around for build failures with GCC 6 backported from upstream glib. +See https://bugzilla.gnome.org/761550 for details. + +diff -Nrup pkg-config-0.29.1.orig/glib/glib/gdate.c pkg-config-0.29.1/glib/glib/gdate.c +--- pkg-config-0.29.1.orig/glib/glib/gdate.c 2016-01-24 22:51:38.000000000 +0100 ++++ pkg-config-0.29.1/glib/glib/gdate.c 2017-02-07 17:34:54.372617599 +0100 +@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate * + * + * Returns: number of characters written to the buffer, or 0 the buffer was too small + */ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wformat-nonliteral" ++ + gsize + g_date_strftime (gchar *s, + gsize slen, +@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s, + return retval; + #endif + } ++ ++#pragma GCC diagnostic pop -- GitLab From c3def62161b75ed733478aadd83675e4bfbcf79b Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 8 Feb 2017 14:27:48 +0100 Subject: [PATCH 211/818] smoldyn --- .../s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb new file mode 100644 index 0000000000..71310f26f2 --- /dev/null +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Smoldyn' +version = '2.48' + +homepage = 'http://www.smoldyn.org/' +description = """ +Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.smoldyn.org/'] +sources = ['smoldyn-%(version)s.tgz'] + +builddependencies = [ + ('CMake', '3.4.3'), + ('LibTIFF','4.0.6'), + ('zlib', '1.2.8'), + ('freeglut', '3.0.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6') +] + +dependencies = [ + ('LibTIFF','4.0.6'), + ('zlib', '1.2.8'), + ('freeglut', '3.0.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6') +] + + +sanity_check_paths = { + 'files': ["bin/smoldyn"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 9943419d1751374d5dce9fb3c799dbc0b17b59ab Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 9 Feb 2017 10:17:10 +0100 Subject: [PATCH 212/818] Add Bison and gettext as build dependencies --- easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb | 2 ++ easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb | 2 ++ easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb index ca30f6a696..94c5bfdb69 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb @@ -18,6 +18,8 @@ source_urls = [ builddependencies = [ ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.4'), ('pkg-config', '0.29.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb index c44e65c206..fbaa5cf2db 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb @@ -18,6 +18,8 @@ source_urls = [ builddependencies = [ ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), ('pkg-config', '0.29.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index 556bda9f6e..586cdcf5d6 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -18,6 +18,8 @@ source_urls = [ builddependencies = [ ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), ('pkg-config', '0.29.1'), ] dependencies = [ -- GitLab From 1e581b8020df5f7d38333ea148b710d93f38d61f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 9 Feb 2017 11:38:22 +0100 Subject: [PATCH 213/818] Emacs with foss2016a --- .../e/Emacs/Emacs-25.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb new file mode 100644 index 0000000000..3b50903d7f --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '25.1' + +homepage = 'http://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor—and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language + with extensions to support text editing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +osdependencies = [ + ('ncurses'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.23'), + ('libjpeg-turbo', '1.5.0'), + ('ncurses', '6.0'), +] + +configopts = '--with-gif=no --with-tiff=no --with-x-toolkit=no --with-xpm=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 97c566f492c41b47976aedb88f1ffe5ad77c38d3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 9 Feb 2017 12:51:50 +0100 Subject: [PATCH 214/818] rm builddep --- easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb index 3b50903d7f..bc3043a68b 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb @@ -13,10 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -osdependencies = [ - ('ncurses'), -] - dependencies = [ ('zlib', '1.2.8'), ('libpng', '1.6.23'), -- GitLab From 3b9db641f233dbf157d15c2aa51f79d20846ca0b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 9 Feb 2017 13:29:58 +0100 Subject: [PATCH 215/818] libdrm: clean up dependencies --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb | 2 -- easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb index bd2875fe53..5d9e8ac938 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016b'} dependencies = [ ('X11', '20160819'), - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb index 1f6c3d5a42..9fb07a2954 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016b'} dependencies = [ ('X11', '20160819'), - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.4'), ] sanity_check_paths = { -- GitLab From bcfcb50c38b30a3cb613d1d3c97cc061d8a5db29 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 9 Feb 2017 12:52:18 +0000 Subject: [PATCH 216/818] update for non cray --- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 30 +++++++++++++++++++ .../easyconfigs/j/Java/Java-1.8.0_121.eb | 15 ++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb new file mode 100644 index 0000000000..81fd376a8e --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -0,0 +1,30 @@ +# @author: Robert Schmidt (OHRI) +# @author: Guilherme Peretti-Pezzi (CSCS) + +easyblock = "CmdCp" + +name = 'Bazel' +version = '0.4.4' + +homepage = 'http://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('Java', '1.8.0_121'), +] + +sources = ['%(namelower)s-%(version)s-dist.zip'] +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] + +files_to_copy = [(['output/bazel'], 'bin')] + +sanity_check_paths={ + 'files': ['bin/bazel'], + 'dirs': ['bin'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb new file mode 100644 index 0000000000..2782d792e8 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = "1.8.0_121" + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 3f6c9e9493b7048cc08631e07b673f8686efdf62 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 9 Feb 2017 14:43:37 +0100 Subject: [PATCH 217/818] adding easyconfigs: GMP-6.1.2-foss-2016b.eb --- .../easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb new file mode 100644 index 0000000000..8f949a1a92 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From a7ea9016be0d7c6c077f075513fbd31f27e4835d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Feb 2017 11:09:29 +0100 Subject: [PATCH 218/818] {vis}[intel/2016b] Ghostscript 9.20 use external freetype, libpng, jpeg, and zlib (REVIEW) --- .../easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index 2238d98b96..d3f76e106a 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -24,6 +24,9 @@ dependencies = [ ('LibTIFF', '4.0.6'), ] +#Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" + configopts = "--with-system-libtiff --enable-dynamic" moduleclass = 'tools' -- GitLab From ee0a56a7b7adb71c4e776ea17e9a17446e6fa064 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Feb 2017 11:38:17 +0100 Subject: [PATCH 219/818] {vis}[foss/2016b] graphviz 0.5.1 w/ Python 2.7.12 (REVIEW) --- .../c/Clang/Clang-3.8.1-foss-2016b.eb | 49 ++++++++++++++ .../c/cairo/cairo-1.14.6-foss-2016b.eb | 40 +++++++++++ ...GObject-Introspection-1.49.1-foss-2016b.eb | 47 +++++++++++++ .../Ghostscript-9.20-foss-2016b.eb | 32 +++++++++ .../g/Graphviz/Graphviz-2.38.0-foss-2016b.eb | 67 +++++++++++++++++++ ...graphviz-0.5.1-foss-2016b-Python-2.7.12.eb | 25 +++++++ .../h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb | 34 ++++++++++ .../p/Pango/Pango-1.40.3-foss-2016b.eb | 31 +++++++++ .../p/pixman/pixman-0.34.0-foss-2016b.eb | 20 ++++++ 9 files changed, 345 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb new file mode 100644 index 0000000000..bc4ee73735 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'foss', 'version': '2016b'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.1'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), + ('libxml2', '2.9.4'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb new file mode 100644 index 0000000000..39aaca6d60 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb new file mode 100644 index 0000000000..76281fb06e --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.49.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('GLib', '2.49.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb new file mode 100644 index 0000000000..7305497c37 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.20' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +sources = ['ghostscript-%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('libjpeg-turbo', '1.5.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('LibTIFF', '4.0.6'), +] + +#Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb new file mode 100644 index 0000000000..0454227509 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.38.0' + +homepage = 'http://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.graphviz.org/pub/graphviz/stable/SOURCES/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('cairo', '1.14.6'), + ('expat', '2.2.0'), + ('freetype', '2.6.5'), + ('Ghostscript', '9.20'), + ('GTS', '0.7.6'), + ('Java', '1.8.0_92', '', True), + ('libpng', '1.6.24'), + ('Pango', '1.40.3'), + ('Perl', '5.24.0'), + ('Qt', '4.8.7'), + ('Tcl', '8.6.5'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('M4', '1.4.17'), + ('SWIG', '3.0.10', '-Python-2.7.12'), +] + +#patches = [ +# 'Graphviz-2.38.0_icc_vmalloc.patch', +# 'Graphviz-2.38.0_icc_sfio.patch', +#] + +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " +configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no ' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +sanity_check_paths = { + 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', + 'lib/libcdt.%s' % SHLIB_EXT, 'lib/libgvc.%s' % SHLIB_EXT, 'lib/libxdot.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/graphviz'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/graphviz/python', + 'CLASSPATH': 'lib/graphviz/java/org/graphviz', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..7290bfdd17 --- /dev/null +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'graphviz' +version = '0.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/graphviz' +description = """Simple Python interface for Graphviz""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('Python', '2.7.12'), + ('Graphviz', '2.38.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb new file mode 100644 index 0000000000..28916e2a3a --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.3.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('freetype', '2.6.5'), +] + +builddependencies = [('GObject-Introspection', '1.49.1')] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb new file mode 100644 index 0000000000..d9bd112b39 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.3' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('X11', '20160819'), + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.3.1'), +] + +builddependencies = [('GObject-Introspection', '1.49.1')] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb new file mode 100644 index 0000000000..9306c63805 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 9c3f6772c903d996b6589cfc3c8f24e6c5022af2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Feb 2017 12:52:48 +0100 Subject: [PATCH 220/818] {vis}[foss/2016b] OpenCV 3.1.0 (REVIEW) --- .../a/ATK/ATK-2.22.0-foss-2016b.eb | 34 ++++++++++ .../f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb | 32 +++++++++ .../g/GTK+/GTK+-2.24.31-foss-2016b.eb | 25 +++++++ .../Gdk-Pixbuf-2.36.0-foss-2016b.eb | 34 ++++++++++ .../j/JasPer/JasPer-1.900.1-foss-2016b.eb | 21 ++++++ .../o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 65 +++++++++++++++++++ .../x/x264/x264-20160614-foss-2016b.eb | 27 ++++++++ .../y/Yasm/Yasm-1.3.0-foss-2016b.eb | 31 +++++++++ 8 files changed, 269 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb new file mode 100644 index 0000000000..357880d140 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.22.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb new file mode 100644 index 0000000000..235a728b8c --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.1.3' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('x264', '20160614'), + ('X11', '20160819'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb new file mode 100644 index 0000000000..c33f283106 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.31' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.22.0'), + ('Gdk-Pixbuf', '2.36.0'), + ('Pango', '1.40.3'), + ('GObject-Introspection', '1.49.1'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb new file mode 100644 index 0000000000..0ffa31b3f4 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.49.1') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb new file mode 100644 index 0000000000..57b073f549 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb new file mode 100644 index 0000000000..df0dfae353 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.1.0' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('FFmpeg', '3.1.3'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('GLib', '2.49.5'), + ('GTK+', '2.24.31'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb b/easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb new file mode 100644 index 0000000000..b44af67ba6 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160614' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb new file mode 100644 index 0000000000..d40e39150a --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 8b9c836ff987d76b17964b7001ece60d513c98f9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 10 Feb 2017 17:11:57 +0100 Subject: [PATCH 221/818] Add missing numpy dep --- .../numpy-1.11.1-foss-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100755 easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..23d10a78e7 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +name = 'numpy' +version = '1.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', +] + +dependencies = [ + ('Python', '2.7.12'), +] + +moduleclass = 'math' -- GitLab From 1932c3467cfc0b1758decc73685ce2643f69ce3c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 13 Feb 2017 13:42:55 +0100 Subject: [PATCH 222/818] adding easyconfigs: disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb --- ...iguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..08032c986d --- /dev/null +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "PythonPackage" + +name = 'disambiguate' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/AstraZeneca-NGS/disambiguate" +description = "Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["https://github.com/AstraZeneca-NGS/disambiguate/archive/"] +sources = ["v%(version)s.tar.gz"] + +dependencies = [ + ('Python', '2.7.11'), + ('BamTools', '2.4.0'), + ('zlib', '1.2.8'), + ('Pysam', '0.9.0', versionsuffix), +] + +# this application provides a python implementation and a C++ implementation +# in the postinstallcmds we compile the C++ version +postinstallcmds = ['$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/'] + +# workaround to avoid the import sanity check +options = {'modulename': 'os'} + +sanity_check_paths = { + 'files': ['bin/disambiguate.py', 'bin/disambiguate'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 042334c87be6f297150acc7507478ba63cfa9967 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 13 Feb 2017 14:44:03 +0100 Subject: [PATCH 223/818] Small formatting change. --- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index 9a164bb75c..184119ac43 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -12,6 +12,7 @@ Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. """ + toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': False, 'pic': True} -- GitLab From 1c7a87a90015a6afb50d6e963021d0888f8661eb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 13 Feb 2017 14:49:40 +0100 Subject: [PATCH 224/818] added bamtools dependency --- .../b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..d0e6af59d8 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb @@ -0,0 +1,16 @@ +name = 'BamTools' +version = '2.4.0' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '2.8.12')] + +files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"] + +moduleclass = 'bio' -- GitLab From 694507e94d1d49292f1bf6e584f90a7a81952e37 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 13 Feb 2017 16:08:55 +0100 Subject: [PATCH 225/818] {vis}[mixed] OpenCV 3.1.0 fix ippicv source download and library install (REVIEW) --- .../o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 17 +++++++++++++++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 16 ++++++++++++++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 17 +++++++++++++++-- 3 files changed, 44 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index f835d278f9..c3490d5f5f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] builddependencies = [ ('CMake', '3.5.2'), @@ -34,6 +42,9 @@ dependencies = [ ('GST-plugins-base', '1.6.4'), ] +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -52,6 +63,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index b12504dd19..f247b850d9 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] patches = ['OpenCV-%(version)s_with_IPP.patch'] @@ -35,6 +43,8 @@ dependencies = [ ] preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -54,6 +64,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 896ae67a98..b38d822003 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] patches = ['OpenCV-%(version)s_with_IPP.patch'] @@ -36,6 +44,9 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -54,6 +65,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + -- GitLab From 161806e5c689355cdf17dc83f6dcf795800943e1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 13 Feb 2017 16:12:52 +0100 Subject: [PATCH 226/818] fix ippicv source download and library installation --- .../o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index df0dfae353..261f39024d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] builddependencies = [ ('CMake', '3.5.2'), @@ -32,6 +40,9 @@ dependencies = [ ('GTK+', '2.24.31'), ] +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -50,6 +61,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + -- GitLab From 9c14d4917e06d1fa78aaab60791e75378faf7b94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Feb 2017 12:40:41 +0200 Subject: [PATCH 227/818] adding easyconfigs: likwid-4.2.0-GCCcore-6.3.0.eb --- .../l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a5b92f3bfe --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.2.0' + +homepage = 'http://code.google.com/p/likwid/' +description = """Likwid stands for Like I knew what I am doing. This project contributes easy to use + command line tools for Linux to support programmers in developing high performance multi threaded programs.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['likwid-%(version)s-config-mk.patch'] + +builddependencies = [('binutils', '2.27')] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +maxparallel = 1 + +moduleclass = 'devel' -- GitLab From 17ab69aa0e6c3c836826fed76a7c0e13a93224b1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Feb 2017 13:40:56 +0200 Subject: [PATCH 228/818] Adding the missing patch file --- .../l/likwid/likwid-4.2.0-config-mk.patch | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch new file mode 100644 index 0000000000..735ec88bea --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch @@ -0,0 +1,43 @@ +# Patches the build system +# Ward Poelmans +diff -ur likwid-likwid-4.1.0.orig/config.mk likwid-likwid-4.1.0/config.mk +--- likwid-likwid-4.1.0.orig/config.mk 2016-05-19 13:16:28.000000000 +0200 ++++ likwid-likwid-4.1.0/config.mk 2016-05-19 13:46:33.345284562 +0200 +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++#PREFIX = /usr/local#NO SPACE + + ################################################################# + # Common users do not need to change values below this comment! # +@@ -33,7 +33,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -44,7 +44,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -71,8 +71,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 -- GitLab From c11448fa5948bdbe33f329150e586676daf7e97e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:00:30 +0100 Subject: [PATCH 229/818] adding easyconfigs: Eigen-3.2.10-intel-2016b.eb, Eigen-3.3.2-intel-2016b.eb --- .../easyconfigs/e/Eigen/Eigen-3.2.10-intel-2016b.eb | 13 +++++++++++++ .../easyconfigs/e/Eigen/Eigen-3.3.2-intel-2016b.eb | 13 +++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.10-intel-2016b.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.10-intel-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.10-intel-2016b.eb new file mode 100644 index 0000000000..9ec07e22e9 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.10-intel-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.10' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-intel-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-intel-2016b.eb new file mode 100644 index 0000000000..6cf3aabc3c --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-intel-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.2' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From c79d04f26a0cff111e13016230adf736eb2b3b0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:07:35 +0100 Subject: [PATCH 230/818] adding easyconfigs: fmt-3.0.1-intel-2016b.eb --- .../f/fmt/fmt-3.0.1-intel-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb new file mode 100644 index 0000000000..e2f4a919bb --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '3.0.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' -- GitLab From a45cef8fddf3f1c0b643bc5823f8e0395192da21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:08:01 +0100 Subject: [PATCH 231/818] adding easyconfigs: googletest-1.8.0-intel-2016b.eb --- .../googletest-1.8.0-intel-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2016b.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2016b.eb new file mode 100644 index 0000000000..95b77139af --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.8.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's C++ test framework" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgmock.a', 'lib/libgmock_main.a', 'lib/libgtest.a', 'lib/libgtest_main.a'], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' -- GitLab From d4ca88d5d12880c6f4efce64141d1df222854385 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:24:11 +0100 Subject: [PATCH 232/818] adding easyconfigs: Cantera-2.3.0-intel-2016b-Python-2.7.12.eb --- ...Cantera-2.3.0-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1347cddcd9 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('SUNDIALS', '2.7.0'), + ('Eigen', '3.3.2'), + ('fmt', '3.0.1'), + ('googletest', '1.8.0'), +] +builddependencies = [ + ('SCons', '2.5.1', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + common_opts +runtest = 'test ' + common_opts +buildopts = 'install ' + common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mixmaster'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' -- GitLab From 2d323b10300b35261d5c2492b3e83d9d2123f01c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:25:24 +0100 Subject: [PATCH 233/818] adding easyconfigs: OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb --- .../m/MCL/MCL-14.137-intel-2016b.eb | 21 +++++++++++ .../OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb | 36 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb new file mode 100644 index 0000000000..11b922bce7 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/mcl'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..c6b49af363 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'OrthoMCL' +version = '2.0.9' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://orthomcl.org/' +description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] + +patches = ['orthomcl_fix-perl-hashbang.patch'] + +dependencies = [ + # a Perl installation providing the DBI module is required + ('Perl', '5.24.0'), + ('MCL', '14.137'), +] + +sanity_check_paths = { + 'files': ['bin/orthomcl%s' % bin for bin in ['AdjustFasta', 'BlastParser', 'DropSchema', 'DumpPairsFiles', + 'ExtractProteinIdsFromGroupsFile', 'ExtractProteinPairsFromGroupsFile', + 'FilterFasta', 'InstallSchema', 'LoadBlast', 'MclToGroups', 'Pairs', + 'ReduceFasta', 'ReduceGroups', 'RemoveIdenticalGroups', 'Singletons', + 'SortGroupMembersByScore', 'SortGroupsFile']], + 'dirs': ['lib/perl/OrthoMCLEngine'], +} + +modextrapaths = {'PERL5LIB': 'lib/perl'} + +sanity_check_commands = [('perl', '-e "use OrthoMCLEngine::Main::Base"')] + +moduleclass = 'bio' -- GitLab From 79058145b43f9220323e5a2a9f4284b478d94e27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:28:20 +0100 Subject: [PATCH 234/818] fix software name for OrthomCL --- .../OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb} | 14 ++++++-------- .../OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb} | 14 ++++++-------- .../orthomcl_fix-perl-hashbang.patch | 0 3 files changed, 12 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/o/{orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb => OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb} (83%) rename easybuild/easyconfigs/o/{orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb => OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb} (83%) rename easybuild/easyconfigs/o/{orthomcl => OrthoMCL}/orthomcl_fix-perl-hashbang.patch (100%) diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb similarity index 83% rename from easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb rename to easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb index 2cbfe2886f..5b8fd1b338 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb @@ -1,7 +1,8 @@ -easyblock = "Tarball" +easyblock = 'Tarball' -name = 'orthomcl' +name = 'OrthoMCL' version = '2.0.8' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://orthomcl.org/' description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" @@ -9,16 +10,13 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(name)sSoftware-v%(version)s.tar.gz'] -source_urls = ['http://orthomcl.org/common/downloads/software/v%s/' % '.'.join(version.split('.')[:2])] +source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -# a Perl installation providing the DBI module is required -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver), + # a Perl installation providing the DBI module is required + ('Perl', '5.16.3'), ('MCL', '12.135'), ] diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb similarity index 83% rename from easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb rename to easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb index 2fe0311606..238ebe881b 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb @@ -1,7 +1,8 @@ -easyblock = "Tarball" +easyblock = 'Tarball' -name = 'orthomcl' +name = 'OrthoMCL' version = '2.0.8' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://orthomcl.org/' description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" @@ -9,16 +10,13 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['%(name)sSoftware-v%(version)s.tar.gz'] -source_urls = ['http://orthomcl.org/common/downloads/software/v%s/' % '.'.join(version.split('.')[:2])] +source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -# a Perl installation providing the DBI module is required -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver), + # a Perl installation providing the DBI module is required + ('Perl', '5.16.3'), ('MCL', '12.135'), ] diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl_fix-perl-hashbang.patch b/easybuild/easyconfigs/o/OrthoMCL/orthomcl_fix-perl-hashbang.patch similarity index 100% rename from easybuild/easyconfigs/o/orthomcl/orthomcl_fix-perl-hashbang.patch rename to easybuild/easyconfigs/o/OrthoMCL/orthomcl_fix-perl-hashbang.patch -- GitLab From 062cef1bbf0eaa24b4cfb9fc2d031dad4b0b0f8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:29:15 +0100 Subject: [PATCH 235/818] enable -fPIC --- easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb index e2f4a919bb..38241af81f 100644 --- a/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-2016b.eb @@ -7,6 +7,7 @@ homepage = 'http://fmtlib.net/' description = "fmt (formerly cppformat) is an open-source formatting library." toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] sources = ['fmt-%(version)s.zip'] -- GitLab From e657761ef99ebeb760d351404dd867448cba4a11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 19:10:59 +0100 Subject: [PATCH 236/818] fix sources spec --- .../o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb index 5b8fd1b338..b0f832c53a 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb @@ -9,7 +9,7 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +sources = ['%(namelower)sSoftware-v%(version)s.tar.gz'] source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb index 238ebe881b..2f54ba6ec5 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb @@ -9,7 +9,7 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'ictce', 'version': '5.3.0'} -sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +sources = ['%(namelower)sSoftware-v%(version)s.tar.gz'] source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -- GitLab From f410c5f9d8a9506ea039409a066d860ec5cb8e7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 19:11:57 +0100 Subject: [PATCH 237/818] fix sources spec in OrthoMCL easyconfig --- .../o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb index c6b49af363..31aa43dbba 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb @@ -9,7 +9,7 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'intel', 'version': '2016b'} -sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +sources = ['%(namelower)sSoftware-v%(version)s.tar.gz'] source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -- GitLab From 867434e5a6957fcc9685beaa3b4f59ed60d3733a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 15 Feb 2017 11:01:55 +0100 Subject: [PATCH 238/818] DMTCP 2.5.0 with foss 2016a --- .../d/DMTCP/DMTCP-2.5.0-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb new file mode 100644 index 0000000000..3f64420e2e --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '2.5.0' + +homepage = "http://dmtcp.sourceforge.net/index.html" +description = """DMTCP (Distributed MultiThreaded Checkpointing) +transparently checkpoints a single-host or distributed computation +in user-space -- with no modifications to user code or to the O/S.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' + -- GitLab From b1f42dea4affc87dda18850e35a79f63dca4d1dc Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 15 Feb 2017 11:09:29 +0100 Subject: [PATCH 239/818] Stacks 1.44 with foss-2016a --- .../s/Stacks/Stacks-1.44-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb new file mode 100644 index 0000000000..6ef7429937 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.44' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose + of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 873bad384198bf5bd300d11b4297db759e803b03 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 15 Feb 2017 11:11:02 +0100 Subject: [PATCH 240/818] Vim 8.0 with foss 2016a --- .../v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1caa37ba7a --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '8.0' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.vim.org/pub/vim/unix/'] +sources = [SOURCELOWER_TAR_BZ2] + +# this dependencies are required for --enable-pythoninterp=yes and --enable-perlinterp=yes to work +# check enabled features running "vim --version" after compilation +dependencies = [ + ('Python', '2.7.11'), + ('Perl', '5.22.1', '-bare') + ] +#osdependencies = ['python','perl-devel'] + +configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim','bin/vimdiff'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a1c0fe373c8123e1474daef7a0857ba72818617d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2017 13:08:30 +0100 Subject: [PATCH 241/818] adding easyconfigs: PEAR-0.9.8-intel-2016b.eb --- .../p/PEAR/PEAR-0.9.8-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb new file mode 100644 index 0000000000..33e09a2ad6 --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.8' + +homepage = 'http://sco.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +checksums = ['1ab079a2cea61aee816012966b7ccacd'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From bac77786fe50b626ed263a3adcaa8734bdda36a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2017 14:26:36 +0100 Subject: [PATCH 242/818] add easyconfigs for Boost & SCons (build) deps of Cantera --- .../Boost-1.63.0-intel-2016b-Python-2.7.12.eb | 23 ++++++++++++++++++ .../SCons-2.5.1-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..b110a50dba --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..6df761e722 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From c261e36bb0a467bd6d270faf48f9304f729b568a Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 15 Feb 2017 16:23:29 +0000 Subject: [PATCH 243/818] updating with review feedback --- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index 81fd376a8e..2c824e618b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -12,19 +12,20 @@ It is used to build the majority of Google's software.""" toolchain = {'name': 'dummy', 'version': ''} +sources = ['%(namelower)s-%(version)s-dist.zip'] +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] + dependencies = [ ('Java', '1.8.0_121'), ] -sources = ['%(namelower)s-%(version)s-dist.zip'] -source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] -cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] +cmds_map = [('.*', "JAVA_VERSION=%(javashortver)s CC=gcc CXX=g++ ./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] sanity_check_paths={ - 'files': ['bin/bazel'], - 'dirs': ['bin'], + 'dirs': ['bin'], + 'files': ['bin/bazel'] } moduleclass = 'devel' -- GitLab From e076db3cc515038c54c49ecd3dc4a6543c4783f6 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 15 Feb 2017 19:11:34 +0000 Subject: [PATCH 244/818] update per review --- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index 2c824e618b..dd70600323 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -19,13 +19,13 @@ dependencies = [ ('Java', '1.8.0_121'), ] -cmds_map = [('.*', "JAVA_VERSION=%(javashortver)s CC=gcc CXX=g++ ./compile.sh")] +cmds_map = [('.*', "./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] sanity_check_paths={ - 'dirs': ['bin'], - 'files': ['bin/bazel'] + 'files': ['bin/bazel'], + 'dirs': [], } moduleclass = 'devel' -- GitLab From 1331efc4299668ef27b7ebbb87bbd217b7b39825 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 15 Feb 2017 21:44:17 +0000 Subject: [PATCH 245/818] modified source url for MCR R2013a and b --- easybuild/easyconfigs/m/MCR/MCR-R2013a.eb | 2 +- easybuild/easyconfigs/m/MCR/MCR-R2013b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb index caffaedaa3..2df01756bc 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb index ea139590d9..4d025dab9a 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -- GitLab From d30b6d06cff6eef14665c45a9c14229aa1cd7b39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 16 Feb 2017 08:28:51 +0100 Subject: [PATCH 246/818] added RNAz for GCC 5 and above GCC changed the default C standard from gnu89 to gnu11, RNAz needs gnu89 --- .../easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb new file mode 100644 index 0000000000..bdf32dd367 --- /dev/null +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'RNAz' +version = '2.1' + +homepage = 'http://www.tbi.univie.ac.at/~wash/RNAz/' +description = """RNAz is a program for predicting structurally conserved and +thermodynamically stable RNA secondary structures in multiple sequence alignments.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +buildopts = 'CFLAGS="-std=gnu89 $CFLAGS"' + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] + +sanity_check_paths = { + 'files': ['bin/RNAz'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 972efb3ff93db5861f76d3ff71e79e7cc73143f6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 09:34:36 +0100 Subject: [PATCH 247/818] Add configurations for GCCcore-6.3.0 and intel-2017a --- .../pkg-config-0.29.1-GCCcore-6.3.0.eb | 30 +++++++++++++++++++ .../pkg-config-0.29.1-intel-2017a.eb | 27 +++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..5cd807b0de --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +patches = [ + 'pkg-config-%(version)s_gcc-6.patch', +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb new file mode 100644 index 0000000000..25371013eb --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 201cc133fb10dfb11c9d5b7e6877535c8d8180dd Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 09:48:32 +0100 Subject: [PATCH 248/818] Add missing builddep on binutils --- .../p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb index 5cd807b0de..dadba07804 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -17,6 +17,11 @@ patches = [ 'pkg-config-%(version)s_gcc-6.patch', ] +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + # don't use PAX, it might break. tar_config_opts = True -- GitLab From a9ec4e655b47953fbb7bc916dfebca9d120361e5 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 10:55:29 +0100 Subject: [PATCH 249/818] Updated X11 bundle and dependencies for GCCcore-6.3.0: - Bumped components to the latest available versions - Added libXfont2 --- .../a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb | 29 ++++ .../a/Automake/Automake-1.15-GCCcore-6.3.0.eb | 36 +++++ .../Autotools-20150215-GCCcore-6.3.0.eb | 18 +++ .../b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb | 18 +++ .../e/expat/expat-2.2.0-GCCcore-6.3.0.eb | 19 +++ .../fontconfig-2.12.1-GCCcore-6.3.0.eb | 25 ++++ .../freetype/freetype-2.7.1-GCCcore-6.3.0.eb | 29 ++++ .../gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb | 26 ++++ .../easyconfigs/g/gettext/gettext-0.19.8.1.eb | 25 ++++ .../l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb | 29 ++++ .../l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb | 20 +++ .../l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb | 26 ++++ .../n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb | 39 +++++ .../x/X11/X11-20170129-GCCcore-6.3.0.eb | 136 ++++++++++++++++++ .../x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 28 ++++ 15 files changed, 503 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..84aebc0f8f --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..304170650f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9e2d66a8e2 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] +# Pure bundle -- no need to specify 'binutils' used when building GCCcore toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..5ec3bbe0cb --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a67bb4fc20 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2cdc8b58de --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.7.1'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2892f7ffb0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.28'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..6e2d7b23a6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb new file mode 100644 index 0000000000..f1e80cfb3b --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('ncurses', '6.0')] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..7aca3fe451 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.28' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9e72961b6b --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b71554c4df --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..097f0bd4af --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27')] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2e89d51b91 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb @@ -0,0 +1,136 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20170129' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.12.1'), + ('freetype', '2.7.1'), + ('zlib', '1.2.11'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.1'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.1', { # 2017-01-29 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.3', common_specs), # 2009-10-14 + ('bigreqsproto', '1.1.2', common_specs), # 2012-03-23 + ('compositeproto', '0.4.2', common_specs), # 2010-10-30 + ('damageproto', '1.2.1', common_specs), # 2010-10-30 + ('dmxproto', '2.3.1', common_specs), # 2011-01-06 + ('dri2proto', '2.8', common_specs), # 2012-07-11 + ('dri3proto', '1.0', common_specs), # 2013-11-01 + ('fixesproto', '5.0', common_specs), # 2011-03-08 + ('fontsproto', '2.1.3', common_specs), # 2014-04-14 + ('glproto', '1.4.17', common_specs), # 2013-12-10 + ('inputproto', '2.3.2', common_specs), # 2016-04-04 + ('kbproto', '1.0.7', common_specs), # 2015-05-01 + ('presentproto', '1.1', common_specs), # 2017-01-26 + ('randrproto', '1.5.0', common_specs), # 2015-05-17 + ('recordproto', '1.14.2', common_specs), # 2012-03-23 + ('renderproto', '0.11.1', common_specs), # 2010-08-10 + ('resourceproto', '1.2.0', common_specs), # 2011-05-28 + ('scrnsaverproto', '1.2.2', common_specs), # 2012-03-23 + ('videoproto', '2.3.3', common_specs), # 2016-03-11 + ('xcmiscproto', '1.2.2', common_specs), # 2012-03-23 + ('xextproto', '7.3.0', common_specs), # 2013-12-27 + ('xf86bigfontproto', '1.2.0', common_specs), # 2009-08-27 + ('xf86dgaproto', '2.1', common_specs), # 2009-10-01 + ('xf86driproto', '2.1.1', common_specs), # 2011-01-06 + ('xf86vidmodeproto', '2.3.1', common_specs), # 2011-01-06 + ('xineramaproto', '1.2.1', common_specs), # 2011-01-06 + ('xproto', '7.0.31', common_specs), # 2016-09-23 + ('libXau', '1.0.8', common_specs), # 2013-05-24 + ('libXdmcp', '1.1.2', common_specs), # 2015-03-21 + ('xcb-proto', '1.12', common_specs), # 2016-05-18 + ('libxcb', '1.12', common_specs), # 2016-05-18 + ('xtrans', '1.3.5', common_specs), # 2014-09-22 + ('libxkbcommon', '0.7.1', { # 2017-01-18 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.4', common_specs), # 2016-10-04 + ('libXext', '1.3.3', common_specs), # 2014-07-24 + ('libFS', '1.0.7', common_specs), # 2015-05-01 + ('libICE', '1.0.9', common_specs), # 2014-06-07 + ('libSM', '1.2.2', common_specs), # 2013-09-08 + ('libXScrnSaver', '1.2.2', common_specs), # 2012-03-08 + ('libXt', '1.1.5', common_specs), # 2015-05-01 + ('libXmu', '1.1.2', common_specs), # 2013-09-08 + ('libXpm', '3.5.12', common_specs), # 2016-12-15 + ('libXaw', '1.0.13', common_specs), # 2015-05-01 + ('libXfixes', '5.0.3', common_specs), # 2016-10-04 + ('libXcomposite', '0.4.4', common_specs), # 2013-01-03 + ('libXrender', '0.9.10', common_specs), # 2016-10-04 + ('libXcursor', '1.1.14', common_specs), # 2013-05-30 + ('libXdamage', '1.1.4', common_specs), # 2013-01-03 + ('libfontenc', '1.1.3', common_specs), # 2015-05-01 + ('libXfont', '1.5.2', common_specs), # 2016-08-31 + ('libXfont2', '2.0.1', common_specs), # 2015-12-11 + ('libXft', '2.3.2', common_specs), # 2014-06-06 + ('libXi', '1.7.9', common_specs), # 2017-01-23 + ('libXinerama', '1.1.3', common_specs), # 2013-05-31 + ('libXrandr', '1.5.1', common_specs), # 2016-10-04 + ('libXres', '1.0.7', common_specs), # 2013-05-31 + ('libXtst', '1.2.3', common_specs), # 2016-10-04 + ('libXv', '1.0.11', common_specs), # 2016-10-04 + ('libXvMC', '1.0.10', common_specs), # 2016-10-04 + ('libXxf86dga', '1.1.4', common_specs), # 2013-05-31 + ('libXxf86vm', '1.1.4', common_specs), # 2015-02-24 + ('libdmx', '1.1.3', common_specs), # 2013-05-28 + ('libpciaccess', '0.13.4', common_specs), # 2015-05-01 + ('libxkbfile', '1.0.9', common_specs), # 2015-05-01 + ('libxshmfence', '1.2', common_specs), # 2015-01-02 + ('xcb-util', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-image', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-keysyms', '0.4.0', common_specs), # 2014-10-01 + ('xcb-util-renderutil', '0.3.9', common_specs), # 2014-06-13 + ('xcb-util-wm', '0.4.1', common_specs), # 2014-02-19 + ('xcb-util-cursor', '0.1.3', common_specs), # 2016-05-12 +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..0e517cfb0f --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.3' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('gettext', '0.19.8.1', '', True), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From ee6c56245332a6367a33663e56f3f6eae904d981 Mon Sep 17 00:00:00 2001 From: Basil Neff Date: Thu, 16 Feb 2017 11:10:05 +0100 Subject: [PATCH 250/818] Change backticks in the gettext description to build RPM Packages with fpm. EasyBuild fails to create RPM packages with backticks in the description. The backticks are not escaped by EasyBuild or fpm. --- easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb | 2 +- .../easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb | 2 +- 31 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb index e7d30bfac7..400996e08a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb index 686c6f9d40..645bdc29be 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb index adf041c9d3..ccaa5c1d29 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb index 5479e98f23..b9f046449c 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb index 21f6d06397..54b916db8e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb index 68b4d25ce9..000ef4aa2d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb index a1a642076c..eeeccb35d4 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb index b9b28dda44..827716cf97 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb index 238843b206..450a973ebb 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb index a0c6e92339..43c9195057 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb index c49302820d..57381cdd38 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb index 2d3d1e0547..1a7da10440 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb index 7e8ff4e184..27ab692a93 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb index 51c244d3ef..e435d00102 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb index 0dbf6fce3a..246fbea3c6 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb index ed81b95755..11ed30961c 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb index 90c8e2d47d..4ff92c775d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb index 1fdb744032..ac6519ed4a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb index 4aed92d350..859ba0f08f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb index a9b8c4c455..802790cb29 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb index d58aad1970..220b284a16 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb index ce355420b2..902bd2a236 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index 690872c686..79d7c0db22 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb index 4580e48c6a..a61ec3269b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb index 4f86721ed0..57cdaad01b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb index 578b07b38d..8e1eda7fc9 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb index 8e1b03ad2a..13b1f6601b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb index 47b250264e..8f8b64bb6f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb index 91c8cacd60..bcee20f66b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb index 6df1b22caa..8671de264d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb index 45caa1fde8..dd9bbb81e0 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" -- GitLab From e1553722814b3068881671e50a3d0ae2dd4a5227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Feb 2017 11:14:19 +0100 Subject: [PATCH 251/818] stick to old source URL for MCR R2013a --- easybuild/easyconfigs/m/MCR/MCR-R2013a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb index 2df01756bc..caffaedaa3 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', + 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -- GitLab From 1e74088992605614a2b9dbf4a745c4776e6fac39 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 11:37:08 +0100 Subject: [PATCH 252/818] sickle 1.33 foss 2017a --- .../s/sickle/sickle-1.33-foss-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb b/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb new file mode 100644 index 0000000000..aad6c785a5 --- /dev/null +++ b/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'MakeCp' + +name = "sickle" +version = "1.33" + +homepage = 'https://github.com/najoshi/sickle' +description = """ Windowed Adaptive Trimming for fastq files using quality """ + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/najoshi/sickle/archive/'] +sources = ['v%(version)s.tar.gz'] + +files_to_copy = [(['sickle'], 'bin'), "README.md", "test"] + +sanity_check_paths = { + 'files': ['bin/sickle'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 949f36606ae1a3b5566b26e45041854c23f17bd3 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 11:45:30 +0100 Subject: [PATCH 253/818] removed buildependencies --- .../easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb index 71310f26f2..7f6179784c 100644 --- a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -13,15 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.smoldyn.org/'] sources = ['smoldyn-%(version)s.tgz'] -builddependencies = [ - ('CMake', '3.4.3'), - ('LibTIFF','4.0.6'), - ('zlib', '1.2.8'), - ('freeglut', '3.0.0'), - ('libXmu', '1.1.2'), - ('libXi', '1.7.6') -] - dependencies = [ ('LibTIFF','4.0.6'), ('zlib', '1.2.8'), -- GitLab From 51343da1acd9adf8c70f11d3f93c03b86c4b62d4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Feb 2017 13:30:33 +0200 Subject: [PATCH 254/818] Adding patch to install libelpatest. --- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 63 +++++++++++++++++++ .../e/ELPA/install_libelpatest.patch | 11 ++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/ELPA/install_libelpatest.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb new file mode 100644 index 0000000000..fe3eecd918 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2016.05.004' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'install_libelpatest.patch', +] + +builddependencies = [ + ('Autotools', '20150215'), +] + +preconfigopts = 'autoreconf && ' + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +postinstallcmds = [ + 'cp config.h config-f90.h %(installdir)s/share/doc/elpa/examples', +] + +sanity_check_paths = { + 'files': [ + 'lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, + 'lib/libelpa_openmp.a', 'lib/libelpa_openmp.%s' % SHLIB_EXT, + 'lib/libelpatest.a', 'lib/libelpatest.%s' % SHLIB_EXT, + 'lib/libelpatest_openmp.a', 'lib/libelpatest_openmp.%s' % SHLIB_EXT, + 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h', + ], + 'dirs': [ + 'bin', 'include/elpa-%(version)s/elpa', + 'include/elpa-%(version)s/modules', 'lib/pkgconfig', + ], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch b/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch new file mode 100644 index 0000000000..2c8f6390ed --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch @@ -0,0 +1,11 @@ +--- Makefile.am.orig 2017-02-16 10:32:55.789545672 +0100 ++++ Makefile.am 2017-02-16 10:33:15.213234461 +0100 +@@ -255,7 +255,7 @@ + build_lib = libelpatest@SUFFIX@.la libelpa@SUFFIX@.la + + # library with shared sources for the test files +-noinst_LTLIBRARIES += libelpatest@SUFFIX@.la ++lib_LTLIBRARIES += libelpatest@SUFFIX@.la + libelpatest@SUFFIX@_la_FCFLAGS = $(AM_FCFLAGS) @FC_MODOUT@private_modules @FC_MODINC@private_modules + libelpatest@SUFFIX@_la_SOURCES = \ + test/shared/util.F90 \ -- GitLab From 59be6a908dfd1ba7cd0778e5096573de5ba8472c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 16 Feb 2017 13:34:40 +0100 Subject: [PATCH 255/818] added requested changes used toolchain option cstd instead of buildopts removed toolchain option optarch changed name template --- easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb index bdf32dd367..4ff67a0efb 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb @@ -10,12 +10,10 @@ description = """RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'optarch': True, 'pic': True} - -buildopts = 'CFLAGS="-std=gnu89 $CFLAGS"' +toolchainopts = {'cstd': 'gnu89', 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] +source_urls = ['http://www.tbi.univie.ac.at/~wash/%(name)s'] sanity_check_paths = { 'files': ['bin/RNAz'], -- GitLab From 055afec64649e52a63df8d499f1d82e7ab720789 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 14:29:53 +0100 Subject: [PATCH 256/818] requested changes --- .../s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb index 7f6179784c..fc06a65970 100644 --- a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -4,8 +4,11 @@ name = 'Smoldyn' version = '2.48' homepage = 'http://www.smoldyn.org/' -description = """ -Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system. +description = """Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of +interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats +other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real +time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real +biological system. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -13,12 +16,16 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.smoldyn.org/'] sources = ['smoldyn-%(version)s.tgz'] +builddependencies = [ + ('CMake', '3.4.3') +] + dependencies = [ - ('LibTIFF','4.0.6'), - ('zlib', '1.2.8'), - ('freeglut', '3.0.0'), - ('libXmu', '1.1.2'), - ('libXi', '1.7.6') + ('LibTIFF','4.0.6'), + ('zlib', '1.2.8'), + ('freeglut', '3.0.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6') ] -- GitLab From e81eab07bf42f6f4cdab2184e9625c49ff01d264 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 14:32:30 +0100 Subject: [PATCH 257/818] Removed backticks in gettest description --- .../easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb index 6e2d7b23a6..c366761771 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8.1' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb index f1e80cfb3b..ee5718ec11 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8.1' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" -- GitLab From c247db112687dc657a726cce723e2f43ae70377a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Feb 2017 17:11:38 +0200 Subject: [PATCH 258/818] Rename the patchfile to match the version of ELPA. --- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 2 +- .../ELPA-2016.05.004_install-libelpatest.patch | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index fe3eecd918..2c6c725788 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -22,7 +22,7 @@ source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'install_libelpatest.patch', + '%(name)s-%(version)s_install-libelpatest.patch', ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch new file mode 100644 index 0000000000..61ac356266 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch @@ -0,0 +1,16 @@ +Change the Makefile.am so that libelpatest gets installed too. +This makes it easier to build the examples. + +Åke Sandgren, HPC2N +diff -ru elpa-2016.05.004.orig/Makefile.am elpa-2016.05.004/Makefile.am +--- elpa-2016.05.004.orig/Makefile.am 2016-10-25 07:13:46.000000000 +0200 ++++ elpa-2016.05.004/Makefile.am 2017-02-16 16:04:40.976781413 +0100 +@@ -255,7 +255,7 @@ + build_lib = libelpatest@SUFFIX@.la libelpa@SUFFIX@.la + + # library with shared sources for the test files +-noinst_LTLIBRARIES += libelpatest@SUFFIX@.la ++lib_LTLIBRARIES += libelpatest@SUFFIX@.la + libelpatest@SUFFIX@_la_FCFLAGS = $(AM_FCFLAGS) @FC_MODOUT@private_modules @FC_MODINC@private_modules + libelpatest@SUFFIX@_la_SOURCES = \ + test/shared/util.F90 \ -- GitLab From 0bd80f7045b1aad79ff905593f5f452c4ea7e417 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Feb 2017 16:13:21 +0100 Subject: [PATCH 259/818] Delete the old non-version specific patch file. --- .../easyconfigs/e/ELPA/install_libelpatest.patch | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 easybuild/easyconfigs/e/ELPA/install_libelpatest.patch diff --git a/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch b/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch deleted file mode 100644 index 2c8f6390ed..0000000000 --- a/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- Makefile.am.orig 2017-02-16 10:32:55.789545672 +0100 -+++ Makefile.am 2017-02-16 10:33:15.213234461 +0100 -@@ -255,7 +255,7 @@ - build_lib = libelpatest@SUFFIX@.la libelpa@SUFFIX@.la - - # library with shared sources for the test files --noinst_LTLIBRARIES += libelpatest@SUFFIX@.la -+lib_LTLIBRARIES += libelpatest@SUFFIX@.la - libelpatest@SUFFIX@_la_FCFLAGS = $(AM_FCFLAGS) @FC_MODOUT@private_modules @FC_MODINC@private_modules - libelpatest@SUFFIX@_la_SOURCES = \ - test/shared/util.F90 \ -- GitLab From 485e058298063893104af9fe5c873cee6628fb14 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 20:06:01 +0100 Subject: [PATCH 260/818] Remove duplicate sources specification --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 2e2eda32d4..c13ef6b657 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -sources = ['openmpi-%(version)s.tar.gz'] + checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -- GitLab From e3d01adc1cf95181b1c90f62d8b6f1395ee7686f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 17 Feb 2017 11:00:39 +0100 Subject: [PATCH 261/818] Make Travis happy --- .../easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb index 1caa37ba7a..69dae180f9 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -7,6 +7,7 @@ easyblock = 'ConfigureMake' name = 'Vim' version = '8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.vim.org' description = """ Vim is an advanced text editor that seeks to provide the power @@ -22,7 +23,7 @@ sources = [SOURCELOWER_TAR_BZ2] dependencies = [ ('Python', '2.7.11'), ('Perl', '5.22.1', '-bare') - ] +] #osdependencies = ['python','perl-devel'] configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' -- GitLab From bab557a4492ce1cc551b85cc34f879ee4e4ad37f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 19 Feb 2017 19:13:22 +0100 Subject: [PATCH 262/818] no comments, space behind ',' --- .../easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb index 69dae180f9..674a6d44d5 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -24,12 +24,11 @@ dependencies = [ ('Python', '2.7.11'), ('Perl', '5.22.1', '-bare') ] -#osdependencies = ['python','perl-devel'] configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' sanity_check_paths = { - 'files': ['bin/vim','bin/vimdiff'], + 'files': ['bin/vim', 'bin/vimdiff'], 'dirs': [], } -- GitLab From 970453d4200d390d1cc7c4eed4d2f3edb7d09c34 Mon Sep 17 00:00:00 2001 From: Sergey Paramonov Date: Sun, 19 Feb 2017 23:37:56 -0500 Subject: [PATCH 263/818] Create Lmod-7.3.eb Lmod 7.3 --- easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb | 28 ++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb b/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb new file mode 100644 index 0000000000..d56882eb94 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Lmod" +version = "7.3" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/TACC/Lmod/archive', + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] + +dependencies = [("Lua", "5.1.4-8")] + +sanity_check_paths = { + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" -- GitLab From 1b5f840316fa864453146d2b77c726f7bf58c097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 12:02:29 +0100 Subject: [PATCH 264/818] adding easyconfigs: StringTie-1.3.3-intel-2017a.eb --- .../StringTie/StringTie-1.3.3-intel-2017a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb new file mode 100644 index 0000000000..aa49a6e1bd --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '1.3.3' + +homepage = 'http://ccb.jhu.edu/software/stringtie/' +description = """StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] + +files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 58a3f10c6d41e8f7a233c700f03ad81ed5c901fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 13:03:50 +0100 Subject: [PATCH 265/818] adding easyconfigs: OpenSSL-1.1.0e-intel-2016a.eb --- .../o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb new file mode 100644 index 0000000000..297ae5a79e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.1.0e' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From fecb6bc94694e55a96bba372d9c7dd0c6635f76e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 13:08:42 +0100 Subject: [PATCH 266/818] adding easyconfigs: Pysam-0.10.0-intel-2016b-Python-2.7.12.eb --- .../c/cURL/cURL-7.52.1-intel-2016b.eb | 31 ++++++++++++++++ .../Pysam-0.10.0-intel-2016b-Python-2.7.12.eb | 36 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb new file mode 100644 index 0000000000..669ee4f2be --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.52.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..624f14ed18 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('cURL', '7.52.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 1a94fbc1ae2bcdf0846d3770f45a6040a26bac32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 13:13:13 +0100 Subject: [PATCH 267/818] fix toolchain spec to intel/2016b for OpenSSL 1.1.0e easyconfig --- ...nSSL-1.1.0e-intel-2016a.eb => OpenSSL-1.1.0e-intel-2016b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/o/OpenSSL/{OpenSSL-1.1.0e-intel-2016a.eb => OpenSSL-1.1.0e-intel-2016b.eb} (92%) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb similarity index 92% rename from easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb rename to easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb index 297ae5a79e..81a9ed4ca3 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb @@ -6,7 +6,7 @@ description = """The OpenSSL Project is a collaborative effort to develop a robu and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. """ -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0058215568b776b205473bae2b5e26fc2a10790a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 14:52:44 +0100 Subject: [PATCH 268/818] remove numpy 1.11.1 easyconfig using Python 2.7.12 since Python installation already includes numpy 1.11.1 --- .../numpy-1.11.1-foss-2016b-Python-2.7.12.eb | 25 ------------------- ...PyTables-3.2.2-foss-2016b-Python-2.7.12.eb | 1 - 2 files changed, 26 deletions(-) delete mode 100755 easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb deleted file mode 100755 index 23d10a78e7..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'numpy' -version = '1.11.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = [ - 'numpy-1.8.0-mkl.patch', -] - -dependencies = [ - ('Python', '2.7.12'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb index 836640b941..fbfabfe34d 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,6 @@ patches = ['pyTables-%(version)s-fix-libs.patch'] dependencies = [ ('Python', '2.7.12'), - ('numpy', '1.11.1', versionsuffix), ('numexpr', '2.6.1', versionsuffix), ('HDF5', '1.8.17'), ] -- GitLab From 9c423e6dcf5e01b5d218859ad432f6fa9d037a33 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 20 Feb 2017 15:13:35 +0100 Subject: [PATCH 269/818] Removed setting of optarch to disabled, which was used during debugging. --- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index 184119ac43..ef1b4dd449 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -14,7 +14,7 @@ and Learning Center (BVLC) and community contributors. """ toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': False, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/BVLC/caffe/archive/'] -- GitLab From 0c61800c9ea6bef57ee64a528744990e2e1163b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:14:32 +0100 Subject: [PATCH 270/818] fix definition of buildopts/installopts in Cantera easyconfig --- .../c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb index df2115bf2e..6ba32558a2 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb @@ -26,7 +26,7 @@ common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lap common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' buildopts = 'build ' + common_opts runtest = 'test ' + common_opts -buildopts = 'install ' + common_opts +installopts = 'install ' + common_opts prefix_arg = 'prefix=' modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From b6b0b3109f6ad009ea0a387602461e56a0f3e348 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:16:24 +0100 Subject: [PATCH 271/818] fix buildopts/installopts in Cantera easyconfig + add patches to fix/skip broken tests --- ...Cantera-2.3.0-intel-2016b-Python-2.7.12.eb | 8 +- .../c/Cantera/Cantera-2.3.0_fix-bug-416.patch | 138 ++++++++++++++++++ .../Cantera-2.3.0_skip-broken-tests.patch | 25 ++++ 3 files changed, 170 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb index 1347cddcd9..594203f790 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb @@ -8,10 +8,16 @@ homepage = 'https://github.com/Cantera/cantera' description = """Chemical kinetics, thermodynamics, and transport tool suite""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} source_urls = ['https://github.com/Cantera/cantera/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + 'Cantera-%(version)s_fix-bug-416.patch', + 'Cantera-%(version)s_skip-broken-tests.patch', +] + dependencies = [ ('Python', '2.7.12'), ('Boost', '1.63.0', versionsuffix), @@ -29,7 +35,7 @@ common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lap common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' buildopts = 'build ' + common_opts runtest = 'test ' + common_opts -buildopts = 'install ' + common_opts +installopts = 'install ' + common_opts prefix_arg = 'prefix=' modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch new file mode 100644 index 0000000000..74efe309f7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch @@ -0,0 +1,138 @@ +backport of fix for broken tests, see https://github.com/Cantera/cantera/issues/416 and https://github.com/Cantera/cantera/pull/430 + +From 0a1257daed71fdd621ac25bcdeea911d84036bfd Mon Sep 17 00:00:00 2001 +From: Ray Speth +Date: Mon, 13 Feb 2017 17:35:35 -0500 +Subject: [PATCH] Stream input to ctml_writer to avoid command line length + limits + +Resolves #416. +--- + src/base/ct2ctml.cpp | 84 ++++++++++------------------------------------------ + 1 file changed, 15 insertions(+), 69 deletions(-) + +diff --git a/src/base/ct2ctml.cpp b/src/base/ct2ctml.cpp +index f04e58f..687fcba 100644 +--- a/src/base/ct2ctml.cpp ++++ b/src/base/ct2ctml.cpp +@@ -18,8 +18,6 @@ + + #ifdef _WIN32 + #include +-#else +-#include + #endif + + using namespace std; +@@ -82,14 +80,6 @@ void ct2ctml(const char* file, const int debug) + static std::string call_ctml_writer(const std::string& text, bool isfile) + { + std::string file, arg; +- bool temp_file_created = false; +- std::string temp_cti_file_name = std::tmpnam(nullptr); +- +- if (temp_cti_file_name.find('\\') == 0) { +- // Some versions of MinGW give paths in the root directory. Using the +- // current directory is more likely to succeed. +- temp_cti_file_name = "." + temp_cti_file_name; +- } + + if (isfile) { + file = text; +@@ -99,44 +89,6 @@ static std::string call_ctml_writer(const std::string& text, bool isfile) + arg = "text=r'''" + text + "'''"; + } + +- // If the user wants to convert a mechanism using a text passed via the +- // source="""...""" +- // argument in python, then we have to make sure that it is short enough +- // to fit in the command line when routed to python as: +- // python -c ... +- // statement downstream in the code +- +- // So, check the max size of a string that can be passed on the command line +- // This is OS Specific. *nix systems have the sysconf() function that tells +- // us the largest argument we can pass. Since such a function does not exist +- // for Windows, we set a safe limit of 32 kB +- +-#ifdef _WIN32 +- long int max_argv_size = 32768; +-#else +- long int max_argv_size = sysconf(_SC_ARG_MAX); +-#endif +- +- if (text.size() > static_cast(max_argv_size) - 500) { +- // If the file is too big to be passed as a command line argument later +- // in the file, then create a temporary file and execute this function +- // as though an input file was specified as the source. +- // We assume the text passed + 500 chars = total size of argv +- +- ofstream temp_cti_file(temp_cti_file_name); +- +- if (temp_cti_file) { +- temp_cti_file << text; +- file = temp_cti_file_name; +- arg = "r'" + file + "'"; +- temp_file_created = true; +- } else { +- // If we are here, then a temp file could not be created +- throw CanteraError("call_ctml_writer", "Very long source argument. " +- "Error creating temporary file '{}'", temp_cti_file_name); +- } +- } +- + #ifdef HAS_NO_PYTHON + //! Section to bomb out if python is not present in the computation + //! environment. +@@ -151,21 +103,23 @@ static std::string call_ctml_writer(const std::string& text, bool isfile) + exec_stream_t python; + python.set_wait_timeout(exec_stream_t::s_all, 1800000); // 30 minutes + stringstream output_stream, error_stream; +- std::vector args; +- args.push_back("-c"); ++ python.start(pypath(), ""); ++ ostream& pyin = python.in(); + +- args.push_back( +- "from __future__ import print_function\n" +- "import sys\n" +- "try:\n" +- " from cantera import ctml_writer\n" +- "except ImportError:\n" +- " print('sys.path: ' + repr(sys.path) + '\\n', file=sys.stderr)\n" +- " raise\n" +- "ctml_writer.convert(" + arg + ", outName='STDOUT')\n" +- "sys.exit(0)\n"); ++ pyin << "from __future__ import print_function\n" ++ "if True:\n" ++ " import sys\n" ++ " try:\n" ++ " from cantera import ctml_writer\n" ++ " except ImportError:\n" ++ " print('sys.path: ' + repr(sys.path) + '\\n', file=sys.stderr)\n" ++ " raise\n" ++ " ctml_writer.convert("; ++ pyin << arg << ", outName='STDOUT')\n"; ++ pyin << " sys.exit(0)\n\n"; ++ pyin << "sys.exit(7)\n"; + +- python.start(pypath(), args.begin(), args.end()); ++ python.close_in(); + std::string line; + + while (python.out().good()) { +@@ -221,14 +175,6 @@ static std::string call_ctml_writer(const std::string& text, bool isfile) + writelog(message.str()); + } + +- if (temp_file_created) { +- // A temp file was created and has to be removed +- bool status = std::remove(temp_cti_file_name.c_str()); +- if (status) { +- writelog("WARNING: Error removing tmp file {}\n", temp_cti_file_name); +- } +- } +- + return python_output; + } + diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch new file mode 100644 index 0000000000..d3b26cf18f --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch @@ -0,0 +1,25 @@ +skip broken test, fails due to strict floating-point value comparison +see https://github.com/Cantera/cantera/issues/433 + +author: Kenneth Hoste (HPC-UGent) + +--- test/kinetics/kineticsFromScratch.cpp.orig 2017-02-15 16:32:24.518921570 +0100 ++++ test/kinetics/kineticsFromScratch.cpp 2017-02-15 16:32:38.509147212 +0100 +@@ -453,7 +453,7 @@ + } + }; + +-TEST_F(KineticsAddSpecies, add_species_sequential) ++/*TEST_F(KineticsAddSpecies, add_species_sequential) + { + ASSERT_EQ((size_t) 0, kin.nReactions()); + +@@ -480,7 +480,7 @@ + p.addSpecies(species["HO2"]); + kin.addReaction(reactions[4]); + check_rates(5, "O:0.01, H2:0.1, H:0.02, OH:0.03, O2:0.4, AR:0.3, H2O2:0.03, HO2:0.01"); +-} ++}*/ + + TEST_F(KineticsAddSpecies, add_species_err_first) + { -- GitLab From a7cb22ec88506b3657bbd7301146e86f3da462ef Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 20 Feb 2017 16:24:46 +0100 Subject: [PATCH 272/818] comment removed --- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb index 0454227509..ef9c393d1a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -35,11 +35,6 @@ builddependencies = [ ('SWIG', '3.0.10', '-Python-2.7.12'), ] -#patches = [ -# 'Graphviz-2.38.0_icc_vmalloc.patch', -# 'Graphviz-2.38.0_icc_sfio.patch', -#] - preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' -- GitLab From 488878acc274064fc674e9c66a166982e19ace76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:38:31 +0100 Subject: [PATCH 273/818] adding easyconfigs: CMake-3.7.2-intel-2016b.eb --- .../c/CMake/CMake-3.7.2-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb new file mode 100644 index 0000000000..2c33988a54 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9c059fcd9caf2012c038c6ff4a5ed575e02762a0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 20 Feb 2017 16:43:53 +0100 Subject: [PATCH 274/818] style changes and sanity check added --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 +++- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 +++- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index c3490d5f5f..5b1245248a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -43,7 +43,8 @@ dependencies = [ ] #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -68,6 +69,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index f247b850d9..bd5181fa1c 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -44,7 +44,8 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -69,6 +70,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index b38d822003..e7f6df5043 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -45,7 +45,8 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -70,6 +71,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } -- GitLab From 3f4f319516313cd0929d18752d148e428851a0c8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 20 Feb 2017 16:47:12 +0100 Subject: [PATCH 275/818] style changes and sanity check added --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 261f39024d..7d801b065b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -41,7 +41,8 @@ dependencies = [ ] #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ppicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -66,6 +67,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } -- GitLab From e5f70be0bf3385ce2a84f2d4f81460c2ea6a856a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:58:51 +0100 Subject: [PATCH 276/818] adding easyconfigs: Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb --- ...dillo-7.800.0-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..509aa4c19a --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Armadillo' +version = '7.800.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://sourceforge.net/projects/arma/files'] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('arpack-ng', '3.4.0'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.7.2')] + +moduleclass = 'numlib' -- GitLab From e883359e8f8a008c4a46f0347a9b7c44b2a825cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 17:02:22 +0100 Subject: [PATCH 277/818] use http rather than ftp source URLs in CFITSIO easyconfigs --- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb index 8c90ec640b..df0d72298b 100755 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} srcversion = version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb index 9a156bffea..79b1be118d 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb index bf8fb571c8..a6a8529f92 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb index acdf7bfb8d..b205f7fd1f 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb index 177bb20dcc..32bbb18488 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb index 08e0bf1795..32720c1e1c 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb index 654a6284e8..4ea772d549 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb index 6291c97147..d7830dc633 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { -- GitLab From f3d0f859cfb5f742029a92697b56d5a930d5d58f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 17:46:00 +0100 Subject: [PATCH 278/818] adding easyconfigs: ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb, PCRE-8.40-intel-2016b.eb, CFITSIO-3.41-intel-2016b.eb --- .../c/CFITSIO/CFITSIO-3.41-intel-2016b.eb | 22 ++++++++ .../p/PCRE/PCRE-8.40-intel-2016b.eb | 20 +++++++ ...ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb | 55 +++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb new file mode 100644 index 0000000000..382c9e2061 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.41' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb new file mode 100644 index 0000000000..136a1027bb --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2ddf7531c8 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = 'v6.06.02' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.3'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), + ('CFITSIO', '3.41'), + ('freetype', '2.6.5'), + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('GL2PS', '1.3.9'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX11/lib' +configopts += ' --with-xft-libdir=$EBROOTX11/lib' +configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' + +moduleclass = 'data' -- GitLab From 42b679976f9cfacadddedc7fe079b4674ed701b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 18:21:08 +0100 Subject: [PATCH 279/818] adding easyconfigs: OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb --- .../BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb | 28 +++++++++++++++ .../m/MCL/MCL-02.063-intel-2016b.eb | 23 ++++++++++++ .../OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 35 +++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..d5d219aba4 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,28 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.24.0'), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb b/easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb new file mode 100644 index 0000000000..7cdcdee529 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '02.063' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://orthomcl.org/common/downloads/software/unsupported/v1.4/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] + +preconfigopts = "rm config.cache && " + +sanity_check_paths = { + 'files': ['bin/mcl'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..6820502e94 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'OrthoMCL' +version = '1.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://orthomcl.org/' +description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +mcl_majver = '02' +mcl_minver = '063' +sources = ['ORTHOMCL_V%%(version)s_mcl-%s-%s.tar' % (mcl_majver, mcl_minver)] +source_urls = ['http://orthomcl.org/common/downloads/software/unsupported/v%(version)s'] + +dependencies = [ + # a Perl installation providing the DBI module is required + ('Perl', '5.24.0'), + ('MCL', '%s.%s' % (mcl_majver, mcl_minver)), + ('BioPerl', '1.7.1', versionsuffix), +] + +start_dir = 'ORTHOMCLV%(version)s' + +sanity_check_paths = { + 'files': ['orthomcl_module.pm', 'orthomcl.pl', 'README'], + 'dirs': ['sample_data'], +} + +modextrapaths = {'PERL5LIB': ''} + +sanity_check_commands = [('perl', '-e "use orthomcl_module;"')] + +moduleclass = 'bio' -- GitLab From 63f002eaf7b16555acb0b4f49c61c148850393ea Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 21 Feb 2017 15:22:14 +0000 Subject: [PATCH 280/818] added eb recipe for igraph --- .../igraph-0.7.1-fix-aclocal-version.patch | 43 +++ .../i/igraph/igraph-0.7.1-intel-2016a.eb | 31 +++ .../igraph-0.7.1-no-lapack-no-blas.patch | 259 ++++++++++++++++++ 3 files changed, 333 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch new file mode 100644 index 0000000000..fc7ded594f --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch @@ -0,0 +1,43 @@ +diff -ru igraph-0.7.1.orig/aclocal.m4 igraph-0.7.1/aclocal.m4 +--- igraph-0.7.1.orig/aclocal.m4 2014-04-22 17:54:54.000000000 +0000 ++++ igraph-0.7.1/aclocal.m4 2017-02-21 15:10:50.062279982 +0000 +@@ -1,4 +1,4 @@ +-# generated automatically by aclocal 1.14 -*- Autoconf -*- ++# generated automatically by aclocal 1.15 -*- Autoconf -*- + + # Copyright (C) 1996-2013 Free Software Foundation, Inc. + +@@ -8619,10 +8619,10 @@ + # generated from the m4 files accompanying Automake X.Y. + # (This private macro should not be called outside this file.) + AC_DEFUN([AM_AUTOMAKE_VERSION], +-[am__api_version='1.14' ++[am__api_version='1.15' + dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to + dnl require some minimum version. Point them to the right macro. +-m4_if([$1], [1.14], [], ++m4_if([$1], [1.15], [], + [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl + ]) + +@@ -8638,7 +8638,7 @@ + # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. + # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. + AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], +-[AM_AUTOMAKE_VERSION([1.14])dnl ++[AM_AUTOMAKE_VERSION([1.15])dnl + m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl + _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) +diff -ru igraph-0.7.1.orig/configure igraph-0.7.1/configure +--- igraph-0.7.1.orig/configure 2014-04-22 17:55:00.000000000 +0000 ++++ igraph-0.7.1/configure 2017-02-21 15:10:50.082279777 +0000 +@@ -2532,7 +2532,7 @@ + + + +-am__api_version='1.14' ++am__api_version='1.15' + + ac_aux_dir= + for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb new file mode 100644 index 0000000000..53b27e3fc2 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'igraph' +version = '0.7.1' + +homepage = 'http://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['igraph-%(version)s.tar.gz'] +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] + +# Fix llapack and llblas when compiling with MKL +# Fix aclocal which is hard-coded to version 1.14 +patches = ['igraph-0.7.1-no-lapack-no-blas.patch', 'igraph-0.7.1-fix-aclocal-version.patch'] + +# link against MKL rather than blas/lapack +preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" +configopts = "--with-external-blas=yes --with-external-lapack=yes" + +sanity_check_paths = { + 'files': ['lib/libigraph.so', 'lib/libigraph.la', 'lib/pkgconfig/igraph.pc'] + + ['include/igraph/%s' % x for x in ['igraph_version.h', 'igraph_types.h', 'igraph_constants.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch new file mode 100644 index 0000000000..70635982cf --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch @@ -0,0 +1,259 @@ +diff -ru igraph-0.7.1.orig/configure igraph-0.7.1/configure +--- igraph-0.7.1.orig/configure 2014-04-22 17:55:00.000000000 +0000 ++++ igraph-0.7.1/configure 2017-02-21 15:00:00.398921297 +0000 +@@ -17266,13 +17266,13 @@ + fi + + if test "$internal_blas" = "no"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy_ in -lblas" >&5 +-$as_echo_n "checking for daxpy_ in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy_ in " >&5 ++$as_echo_n "checking for daxpy_ in ... " >&6; } + if ${ac_cv_lib_blas_daxpy_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17307,16 +17307,16 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy in -lblas" >&5 +-$as_echo_n "checking for daxpy in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy in " >&5 ++$as_echo_n "checking for daxpy in ... " >&6; } + if ${ac_cv_lib_blas_daxpy+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17351,16 +17351,16 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY_ in -lblas" >&5 +-$as_echo_n "checking for DAXPY_ in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY_ in " >&5 ++$as_echo_n "checking for DAXPY_ in ... " >&6; } + if ${ac_cv_lib_blas_DAXPY_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17395,16 +17395,16 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY in -lblas" >&5 +-$as_echo_n "checking for DAXPY in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY in " >&5 ++$as_echo_n "checking for DAXPY in ... " >&6; } + if ${ac_cv_lib_blas_DAXPY+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17439,7 +17439,7 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +@@ -17452,8 +17452,8 @@ + + fi + +- LDFLAGS="${LDFLAGS} -lblas" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lblas" ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + + $as_echo "#define INTERNAL_BLAS 1" >>confdefs.h +@@ -17461,13 +17461,13 @@ + fi + + if test "$internal_lapack" = "no"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv_ in -llapack" >&5 +-$as_echo_n "checking for dlarnv_ in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv_ in " >&5 ++$as_echo_n "checking for dlarnv_ in ... " >&6; } + if ${ac_cv_lib_lapack_dlarnv_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17502,16 +17502,16 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv in -llapack" >&5 +-$as_echo_n "checking for dlarnv in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv in " >&5 ++$as_echo_n "checking for dlarnv in ... " >&6; } + if ${ac_cv_lib_lapack_dlarnv+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17546,16 +17546,16 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV_ in -llapack" >&5 +-$as_echo_n "checking for DLARNV_ in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV_ in " >&5 ++$as_echo_n "checking for DLARNV_ in ... " >&6; } + if ${ac_cv_lib_lapack_DLARNV_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17590,16 +17590,16 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV in -llapack" >&5 +-$as_echo_n "checking for DLARNV in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV in " >&5 ++$as_echo_n "checking for DLARNV in ... " >&6; } + if ${ac_cv_lib_lapack_DLARNV+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17634,7 +17634,7 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +@@ -17647,8 +17647,8 @@ + + fi + +- LDFLAGS="${LDFLAGS} -llapack" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -llapack" ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + + $as_echo "#define INTERNAL_LAPACK 1" >>confdefs.h +diff -ru igraph-0.7.1.orig/configure.ac igraph-0.7.1/configure.ac +--- igraph-0.7.1.orig/configure.ac 2014-04-22 13:01:17.000000000 +0000 ++++ igraph-0.7.1/configure.ac 2017-02-21 15:00:00.398921297 +0000 +@@ -235,9 +235,9 @@ + AC_CHECK_LIB([blas], [daxpy], [], + AC_CHECK_LIB([blas], [DAXPY_], [], + AC_CHECK_LIB([blas], [DAXPY], [], +- [AC_MSG_RESULT(not found, trying to use -lblas anyway.)])))) +- LDFLAGS="${LDFLAGS} -lblas" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lblas" ++ [AC_MSG_RESULT(not found, trying to use anyway.)])))) ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + AC_DEFINE([INTERNAL_BLAS], [1], [Define to 1 if you use the internal BLAS library]) + fi +@@ -247,9 +247,9 @@ + AC_CHECK_LIB([lapack], [dlarnv], [], + AC_CHECK_LIB([lapack], [DLARNV_], [], + AC_CHECK_LIB([lapack], [DLARNV], [], +- [AC_MSG_RESULT(not found, trying to use -llapack anyway.)])))) +- LDFLAGS="${LDFLAGS} -llapack" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -llapack" ++ [AC_MSG_RESULT(not found, trying to use anyway.)])))) ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + AC_DEFINE([INTERNAL_LAPACK], [1], [Define to 1 if you use the internal LAPACK library]) + fi +diff -ru igraph-0.7.1.orig/tests/testsuite igraph-0.7.1/tests/testsuite +--- igraph-0.7.1.orig/tests/testsuite 2014-04-22 17:55:15.000000000 +0000 ++++ igraph-0.7.1/tests/testsuite 2017-02-21 15:00:00.417921103 +0000 +@@ -3793,9 +3793,9 @@ + + + { set +x +-$as_echo "$at_srcdir/types.at:136: \$CC \${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I\${abs_top_srcdir}/include -I\${abs_top_srcdir}/src -I\${abs_top_builddir}/include -I\${abs_top_builddir} -L\${abs_top_builddir}/src/.libs -ligraph -lm -lblas -o itest" ++$as_echo "$at_srcdir/types.at:136: \$CC \${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I\${abs_top_srcdir}/include -I\${abs_top_srcdir}/src -I\${abs_top_builddir}/include -I\${abs_top_builddir} -L\${abs_top_builddir}/src/.libs -ligraph -lm -o itest" + at_fn_check_prepare_notrace 'a ${...} parameter expansion' "types.at:136" +-( $at_check_trace; $CC ${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I${abs_top_srcdir}/include -I${abs_top_srcdir}/src -I${abs_top_builddir}/include -I${abs_top_builddir} -L${abs_top_builddir}/src/.libs -ligraph -lm -lblas -o itest ++( $at_check_trace; $CC ${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I${abs_top_srcdir}/include -I${abs_top_srcdir}/src -I${abs_top_builddir}/include -I${abs_top_builddir} -L${abs_top_builddir}/src/.libs -ligraph -lm -o itest + ) >>"$at_stdout" 2>>"$at_stderr" 5>&- + at_status=$? at_failed=false + $at_check_filter +diff -ru igraph-0.7.1.orig/tests/types.at igraph-0.7.1/tests/types.at +--- igraph-0.7.1.orig/tests/types.at 2014-04-15 13:00:46.000000000 +0000 ++++ igraph-0.7.1/tests/types.at 2017-02-21 15:00:00.417921103 +0000 +@@ -133,7 +133,7 @@ + AT_SETUP([Sparse matrix, multiplications (igraph_sparsemat_t): ]) + AT_KEYWORDS([sparse matrix igraph_sparsemat_t]) + AT_COMPILE_CHECK([simple/igraph_sparsemat2.c], [simple/igraph_sparsemat2.out], +- [], [INTERNAL], [-lblas]) ++ [], [INTERNAL], []) + AT_CLEANUP + + AT_SETUP([Sparse matrix, indexing (igraph_sparsemat_t): ]) -- GitLab From 0731bdbd8e8fee86ea385140bf383a8c52e238e8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 21 Feb 2017 16:10:35 +0000 Subject: [PATCH 281/818] fixed naming convention of the easyconfig file --- .../{igraph-0.7.1-intel-2016a.eb => igraph-0.7.1-intel-2016b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/igraph/{igraph-0.7.1-intel-2016a.eb => igraph-0.7.1-intel-2016b.eb} (100%) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb rename to easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb -- GitLab From 5d951ce558039bed7e9cb0b4f74c29aaf268492b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Feb 2017 20:23:57 +0100 Subject: [PATCH 282/818] more style fixes in easyconfigs --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 2 +- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 2 +- .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 4 ++-- .../b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb | 2 +- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 2 +- .../Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb | 2 +- ...fe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 2 +- .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- .../c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 2 +- .../easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb | 2 +- .../g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 2 +- .../i/IOzone/IOzone-3.434-foss-2016a.eb | 8 ++++---- .../Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 2 +- .../Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 2 +- .../l/LevelDB/LevelDB-1.18-foss-2016a.eb | 2 +- .../l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb | 2 +- .../l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb | 2 +- .../l/libpsortb/libpsortb-1.0-foss-2016a.eb | 4 ++-- ...0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- ....67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 2 +- .../m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb | 2 +- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- ...MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb | 2 +- .../m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 4 ++-- .../m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 2 +- .../m/Metal/Metal-2011-03-25-foss-2016a.eb | 4 ++-- .../m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb | 2 +- .../m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 2 +- .../numpy-1.9.2-intel-2016b-Python-2.7.12.eb | 2 +- .../OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 4 ++-- .../p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb | 7 +++---- .../PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 2 +- .../PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 4 ++-- .../PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 8 ++++---- .../p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb | 2 +- .../p/Paraver/Paraver-4.5.6-foss-2015a.eb | 2 +- ...2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 2 +- .../p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb | 6 +++--- .../easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb | 2 +- .../PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 4 ++-- .../PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb | 4 ++-- .../PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb | 4 ++-- .../PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb | 4 ++-- .../p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 2 +- .../p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb | 2 +- ...tobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb | 2 +- ...otobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 2 +- ...tobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb | 2 +- ...otobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb | 2 +- ...obuf-python-3.2.0-intel-2016b-Python-2.7.12.eb | 2 +- ...tobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb | 2 +- .../pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb | 2 +- .../easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb | 6 +++--- .../s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb | 4 ++-- .../s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb | 4 ++-- .../s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 2 +- .../s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 2 +- .../s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb | 15 ++++++--------- .../Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb | 2 +- .../Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb | 2 +- .../s/Stacks/Stacks-1.03-goolf-1.4.10.eb | 4 ++-- .../s/Stacks/Stacks-1.03-ictce-5.3.0.eb | 4 ++-- .../s/Stacks/Stacks-1.40-foss-2016a.eb | 4 ++-- .../s/Stacks/Stacks-1.42-foss-2016a.eb | 4 ++-- .../s/Stacks/Stacks-1.44-foss-2016a.eb | 4 ++-- .../s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb | 2 +- .../s/StringTie/StringTie-1.3.0-intel-2016b.eb | 2 +- .../s/StringTie/StringTie-1.3.3-intel-2017a.eb | 2 +- .../easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb | 2 +- .../scipy-0.16.0-intel-2016b-Python-2.7.12.eb | 2 +- .../s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb | 12 ++++++------ .../stemming-1.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb | 2 +- .../sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb | 4 ++-- .../t/Trinity/Trinity-2.1.1-intel-2015b.eb | 2 +- .../t/Trinity/Trinity-2.2.0-foss-2016a.eb | 2 +- .../USPEX-9.4.4-intel-2016b-Python-2.7.12.eb | 3 +-- .../xcb-util-image-0.4.0-intel-2015b.eb | 2 +- .../z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb | 2 +- .../z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb | 2 +- 95 files changed, 139 insertions(+), 144 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 12d87fd3a6..56456bbd62 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -32,7 +32,7 @@ modextrapaths = { 'PYTHONPATH': ['lib/'] } -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index 33dbe5c739..f21285e25b 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -32,7 +32,7 @@ modextrapaths = { 'PYTHONPATH': ['lib/'] } -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 0dc4a540af..20f57806c7 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -8,13 +8,13 @@ description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -toolchain = {'name': 'foss','version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] dependencies = [ - ('GSL','2.1') + ('GSL', '2.1') ] runtest = 'check' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb index 2490a42529..b13a4f1946 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb @@ -22,7 +22,7 @@ cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] -sanity_check_paths={ +sanity_check_paths = { 'files': ['bin/bazel'], 'dirs': ['bin'], } diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index dd70600323..5bfa2535aa 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -23,7 +23,7 @@ cmds_map = [('.*', "./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] -sanity_check_paths={ +sanity_check_paths = { 'files': ['bin/bazel'], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb index 18a7a4b744..b906f81abf 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -25,6 +25,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index ef1b4dd449..e1484d4027 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -48,7 +48,7 @@ modextrapaths = {'PYTHONPATH': ['python'] } sanity_check_paths = { 'files': ['bin/caffe'] + - ['lib/%s' % x for x in ['libcaffe.so','libproto.a']] + + ['lib/%s' % x for x in ['libcaffe.so', 'libproto.a']] + ['python/caffe/_caffe.so'] + ['include/caffe/proto/caffe.pb.h'], 'dirs': [], diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 549296f08e..a2bd44831e 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ ('Python', '2.7.11'), ] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] +files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb index 2facea57d9..e56c03bf3f 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -19,7 +19,7 @@ sources = ['%(name)s_%(version)s.tgz'] dependencies = [('Boost', '1.60.0')] -builddependencies = [('CMake', '3.4.3',)] +builddependencies = [('CMake', '3.4.3')] start_dir = 'src' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb index 378ea5f63e..634f2c0cf8 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libgsl.so', 'lib/libgsl.a'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb index 3ebc1003fc..0d6323dcef 100644 --- a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCE_ZIP] source_urls = ['https://googletest.googlecode.com/files'] -sanity_check_paths={ +sanity_check_paths = { 'files': ['CMakeLists.txt', ], 'dirs': ['include', 'src'], } diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index 09fb675534..f6d0b1f028 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -24,7 +24,7 @@ files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], - 'dirs': ['bin','doc'] + 'dirs': ['bin', 'doc'] } moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 8bd48f9c2e..9e03233c20 100644 --- a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -19,17 +19,17 @@ buildopts = 'linux-AMD64' files_to_copy = [ (['src/current/iozone'], 'bin'), - (['src/current/%s' % docfile for docfile in ['gengnuplot.sh','report.pl','Changes.txt']],'share/doc'), - (['src/current/%s' % docfile for docfile in ['gengnuplot.sh','Generate_Graphs','gnu3d.dem']],'share'), + (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'report.pl', 'Changes.txt']], 'share/doc'), + (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'Generate_Graphs', 'gnu3d.dem']], 'share'), (['docs/iozone.1'], 'share/man/man1'), - (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc','IOzone_msword_98.pdf','Iozone_ps.gz','Run_rules.doc']], + (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', 'Run_rules.doc']], 'share/doc'), ] sanity_check_paths = { 'files': ['bin/iozone'], - 'dirs': ['bin','share/doc','share/man'] + 'dirs': ['bin', 'share/doc', 'share/man'] } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index 4bb09cbfe2..9a8c7fce6d 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix='-Perl-%(perlver)s' +versionsuffix ='-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb index 8814a7c92c..fc353606af 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix='-Perl-%(perlver)s' +versionsuffix ='-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb index f3fb0f0115..c5eee2ec3d 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb @@ -26,7 +26,7 @@ postinstallcmds=[ sanity_check_paths = { - 'files': ['include/leveldb/cache.h','include/leveldb/table.h', + 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', 'lib/libleveldb.a', 'lib/libleveldb.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb index 173c7dbd1e..534b88561a 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb index ef47d32bbf..deb2164941 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb index 07ee053893..9297cefc7a 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb index 63a5c28598..9301b8c32d 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb index 353bbfd940..fb4f7b4645 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb index a25e47aac4..a61396897c 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb index 41eb85171a..49ee159605 100644 --- a/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb @@ -13,8 +13,8 @@ source_urls = ['http://www.psort.org/download/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['lib64/libhmmer.so','lib64/libsvmloc.so'], + 'files': ['lib64/libhmmer.so', 'lib64/libsvmloc.so'], 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index de510f4adc..9b8ad14bb5 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -11,7 +11,7 @@ description = """MDSplus is a set of software tools for data acquisition and sto toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] -sources = ['stable_release-%s.zip' % version.replace('.','-')] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ ('Java', '1.7.0_79', '', True), diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index 25d836f8e5..9296449814 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -11,7 +11,7 @@ description = """MDSplus is a set of software tools for data acquisition and sto toolchain = {'name': 'goolf', 'version': '1.5.16'} source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] -sources = ['stable_release-%s.zip' % version.replace('.','-')] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ ('Java', '1.7.0_79', '', True), diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb index b6f05aeb5d..25e6d72da5 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb @@ -35,7 +35,7 @@ prebuildopts = 'make mpis && make clean && ' start_dir = 'src' sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['migrate-n','migrate-n-mpi']], + 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], 'dirs': ['man'], } diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index c8deee658d..3bb9c9fb71 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -16,7 +16,7 @@ description = """MPJ Express is an open source Java message passing library that toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] -sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] +sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] builddependencies = [('CMake', '3.5.2')] diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 273c10ebde..8c2cfb12b9 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -15,7 +15,7 @@ description = """MPJ Express is an open source Java message passing library that toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] -sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] +sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] java = 'Java' javaver = '1.7.0_75' diff --git a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb index 3c30407be2..b454981b04 100644 --- a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb @@ -16,7 +16,7 @@ description = """ MaCH 1.0 is a Markov Chain based haplotyper. It can resolve lo toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.sph.umich.edu/csg/abecasis/MaCH/download/'] -sources = ['%s.%s.source.tgz' % (name.lower(), version.replace(".c",""))] +sources = ['%s.%s.source.tgz' % (name.lower(), version.replace('.c', ''))] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb index 250398115a..e008b133f5 100644 --- a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb @@ -16,7 +16,7 @@ description = """ MaCH 1.0 is a Markov Chain based haplotyper. It can resolve lo toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['http://www.sph.umich.edu/csg/abecasis/MaCH/download/'] -sources = ['%s.%s.source.tgz' % (name.lower(), version.replace(".c",""))] +sources = ['%s.%s.source.tgz' % (name.lower(), version.replace('.c', ''))] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index fb2151e5df..231d3ed99e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.67'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 171b47710c..7b54c5a0b7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.67'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3282ad740c..ecd0aaeeb3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.67'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index a919f2eab9..18bebf34fd 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.68'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index 54f7d8a513..09f90b3879 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.68'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb index 8152b5bb38..b8a0ae2d3f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -50,7 +50,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-share sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index 90fd4b0810..d9578ef42b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -50,7 +50,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-share sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb index 6f7d234353..04f7962ec3 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb @@ -16,11 +16,11 @@ source_urls = ['http://csg.sph.umich.edu/abecasis/Metal/download/'] toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} -patches=['Metal-%(version)s_Makefile.patch'] +patches = ['Metal-%(version)s_Makefile.patch'] skipsteps=['configure'] -buildopts='all' +buildopts = 'all' installopts = 'INSTALLDIR=%(installdir)s/bin' diff --git a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb index 79a432c81f..50e766c0ce 100644 --- a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Minimac2' version = '2014.9.15' diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index fdd34a04e1..ba77602cd4 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -21,7 +21,7 @@ skipsteps = ['configure'] preinstallopts = "export EBINSTALLPREFIX=%(installdir)s && " -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libmagma.so', 'lib/libmagma.a'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb index b0f7a1aaf1..4cb1525158 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.12'), ] -# need to use pip rather than regular 'setup.py install,' +# need to use pip rather than regular 'setup.py install' # to ensure that this numpy wins over the one in the Python installation; # using easy_install does not work... use_pip = True diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index d30d6266ab..fbe8f5cfab 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -27,8 +27,8 @@ dependencies = [ options = {'modulename': 'obitools'} sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ['ali2consensus','ecotag','obiaddtaxids','obicount','obistat']], - 'dirs': ['bin','lib/python%(pyshortver)s/site-packages/obitools'], + 'files': ['bin/%s' % binfile for binfile in ['ali2consensus', 'ecotag', 'obiaddtaxids', 'obicount', 'obistat']], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/obitools'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb index b46c6bff0d..c67cbf7de9 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb @@ -25,10 +25,9 @@ dependencies = [ ] sanity_check_paths = { - 'files': - ["bin/%s" % binfile for binfile in ['gp','gp-2.7','gphelp','tex2mail']] + - [ "include/pari/%s" % incfile for incfile in ['pari.h','genpari.h']], - 'dirs': ["bin","include"] + 'files': ['bin/%s' % binfile for binfile in ['gp', 'gp-2.7', 'gphelp', 'tex2mail']] + + ['include/pari/%s' % incfile for incfile in ['pari.h', 'genpari.h']], + 'dirs': ['bin', 'include'] } moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 89ae4df712..32e6adc9b7 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock='Tarball' +easyblock = 'Tarball' name = "PGDSpider" version = "2.1.0.3" diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index bb22d3db40..61cae6188e 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -10,7 +10,7 @@ description = """PLAST is a parallel alignment search tool for comparing large p toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v%(version)s/'] -sources=['%(namelower)s_source_v%(version)s.tar.gz'] +sources = ['%(namelower)s_source_v%(version)s.tar.gz'] builddependencies = [ ('CMake', '3.5.2'), @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': ['include', 'include/algo', 'include/alignment', 'include/misc'], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 79449c632c..b5baf3a55c 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -18,10 +18,10 @@ patches = [ dependencies = [ ('Perl', '5.22.1'), - ('libpsortb','1.0'), - ('BioPerl','1.6.924','-Perl-5.22.1'), - ('BLAST','2.2.26', '-Linux_x86_64', True), - ('pftoolsV3','20160324'), + ('libpsortb', '1.0'), + ('BioPerl', '1.6.924', '-Perl-5.22.1'), + ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('pftoolsV3', '20160324'), ] options = {'modulename': 'Bio::Tools::PSort'} diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb index 298d4bf94a..aabbb0dc24 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -24,6 +24,6 @@ dependencies = [ # http://www.bsc.es/computer-sciences/performance-tools/downloads # Requires input of email address for download -sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.bz2'] +sources = ['%(namelower)s-' + "sources" + '-%(version)s.tar.bz2'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb index 646562570d..f5a5940d0d 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb @@ -27,6 +27,6 @@ dependencies = [ # http://www.bsc.es/computer-sciences/performance-tools/downloads # Requires input of email address for download -sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] +sources = ['%(namelower)s-' + "sources" + '-%(version)s.tar.gz'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index 16cea8d33b..c3b096e84c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -18,7 +18,7 @@ versionsuffix += '-freetype-%s' % freetype_ver dependencies = [ ('Python', '2.7.11'), - ('libjpeg-turbo', '1.4.2','-NASM-2.12.01'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb index 9f312bdd69..7dffcdb458 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -20,11 +20,11 @@ sources = ['%(name)s_v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = [(["platanus"],'bin'), "README", "LICENSE"] +files_to_copy = [(['platanus'], 'bin'), 'README', 'LICENSE'] sanity_check_paths = { - 'files': ["bin/platanus"], - 'dirs': [""], + 'files': ['bin/platanus'], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb index 379bdbc80d..4c23222ada 100644 --- a/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb +++ b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb @@ -21,7 +21,7 @@ configopts = '--disable-latex-doc' postinstallcmds = ["mv %(installdir)s/etc/probabel_config.cfg.example %(installdir)s/etc/probabel_config.cfg"] sanity_check_paths = { - 'files': ['bin/probabel', 'bin/pacoxph', 'bin/palinear', 'bin/palogist','etc/probabel_config.cfg'], + 'files': ['bin/probabel', 'bin/pacoxph', 'bin/palinear', 'bin/palogist', 'etc/probabel_config.cfg'], 'dirs': ['share'], } diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index 1438b0e86a..13ffa9e09b 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ('GLib', '2.48.0'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb index 372e050018..57753b92f3 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ('GLib', '2.49.5'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb index 7383e08e64..4f0ee83679 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ('GLib', '2.48.0'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb index b961fbd0a4..56f61040cd 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ('GLib', '2.49.5'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index 62cd674cc5..dcac389893 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -32,6 +32,6 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] #hidden = True # bare installation: only known module deps for GCCcore tools included -exts_list =[] +exts_list = [] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb index 8d5302dd6c..f72f7b4c0e 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb @@ -1,4 +1,4 @@ -easyblock='ConfigureMake' +easyblock = 'ConfigureMake' name = 'pftoolsV3' version = '20160324' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb index 3deb45334a..986362ad06 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.0.2' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb index 64b04ec53c..fbb897d434 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.0.2' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb index 25a3d48ede..8512c8ff8b 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb index a88f02f65a..c25cad0fae 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb index 136b95fa55..2dd5db9c4e 100755 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb index 89a06c0e60..fa54b7dce0 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index bf649cda81..3b3bd56fa2 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -58,7 +58,7 @@ installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', - 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']] + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb index de615e7620..04ee893a0e 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -builddependencies = [('Python', '2.7.12'), ('CMake','3.6.2')] +builddependencies = [('Python', '2.7.12'), ('CMake', '3.6.2')] sanity_check_paths = { 'files': ['bin/rustc', 'bin/rustdoc'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb index a06ae54597..ed54478e03 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -builddependencies = [('Python', '2.7.12'), ('CMake','3.6.2')] +builddependencies = [('Python', '2.7.12'), ('CMake', '3.6.2')] sanity_check_paths = { 'files': ['bin/rustc', 'bin/rustdoc'], diff --git a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb index 756efd9115..189d1b413d 100644 --- a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -15,9 +15,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '--with-mpi' dependencies = [ - ('XZ','5.2.2'), - ('zlib','1.2.8'), - ('GSL','1.16'), # GSL 2.1 does not work. + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), # GSL 2.1 does not work. ('Boost', '1.61.0'), ] diff --git a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb index 15d6744935..a2a47d4c1e 100644 --- a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb @@ -13,11 +13,11 @@ description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/'] -sources=['%(namelower)s_v%(version)s.tar.gz'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] prebuildopts = 'make clean &&' -files_to_copy = [(['sumaclust'],'bin'),'sumaclust_user_manual.pdf'] +files_to_copy = [(['sumaclust'], 'bin'), 'sumaclust_user_manual.pdf'] sanity_check_paths = { 'files': ['bin/sumaclust', 'sumaclust_user_manual.pdf'], diff --git a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb index 6ad5e46d49..b96f631d9c 100644 --- a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb @@ -13,11 +13,11 @@ description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumatra/uploads/251020bbbd6c6595cb9fce6077e29952/'] -sources=['%(namelower)s_v%(version)s.tar.gz'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] prebuildopts = 'make clean &&' -files_to_copy = [(['sumatra'],'bin'),'sumatra_user_manual.pdf'] +files_to_copy = [(['sumatra'], 'bin'), 'sumatra_user_manual.pdf'] sanity_check_paths = { 'files': ['bin/sumatra', 'sumatra_user_manual.pdf'], diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index d38576ab53..031be8f553 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -9,7 +9,7 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} -sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] +sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] dependencies = [('Java', '1.7.0_79')] diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb index fc06a65970..0d3233c817 100644 --- a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('LibTIFF','4.0.6'), + ('LibTIFF', '4.0.6'), ('zlib', '1.2.8'), ('freeglut', '3.0.0'), ('libXmu', '1.1.2'), diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb index f15b6559ac..6af29bdb8b 100644 --- a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb @@ -14,10 +14,8 @@ easyblock = 'ConfigureMake' name = 'SortMeRNA' version = '2.1' -homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' -description = """ -SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. -""" +homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' +description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,12 +24,11 @@ source_urls = ['https://github.com/biocore/sortmerna/archive/'] sources = ['%(version)s.tar.gz'] # Patch for double includes of header files in Makefile.in -patches=['SortMeRNA-%(version)s_Makefile.in.patch'] - -sanity_check_paths={ - 'files': ['bin/indexdb_rna','bin/sortmerna'], - 'dirs': ['include','sortmerna'] +patches = ['SortMeRNA-%(version)s_Makefile.in.patch'] +sanity_check_paths = { + 'files': ['bin/indexdb_rna', 'bin/sortmerna'], + 'dirs': ['include', 'sortmerna'] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb index e8b9b26666..656bb0f55e 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb @@ -47,7 +47,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], - 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' %version], + 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' % version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work ('sphinx_rtd_theme', '0.1.10a0', { diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb index a58b6b19e0..26cda8da07 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb @@ -47,7 +47,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], - 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' %version], + 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' % version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work ('sphinx_rtd_theme', '0.1.10a0', { diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb index a99ef374cd..5590d0a6b0 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb @@ -5,8 +5,8 @@ version = '1.03' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb index a9bfd6bbb4..005b7b2b57 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb @@ -5,8 +5,8 @@ version = '1.03' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb index 189d7f6db0..197e799318 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb @@ -5,8 +5,8 @@ version = '1.40' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb index 6d5d6358c8..e042becab7 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb @@ -5,8 +5,8 @@ version = '1.42' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb index 6ef7429937..1df7d789c0 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb @@ -5,8 +5,8 @@ version = '1.44' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb index 70ca06ed76..f2c6a5db74 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb @@ -17,7 +17,7 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] - + sanity_check_paths = { 'files': ['bin/stringtie'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb index 424d2b7aeb..69634c30e6 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb @@ -17,7 +17,7 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] - + sanity_check_paths = { 'files': ['bin/stringtie'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb index aa49a6e1bd..2476496f2d 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb @@ -17,7 +17,7 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] - + sanity_check_paths = { 'files': ['bin/stringtie'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb index 512dbbe733..6f12c299b1 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" %SHLIB_EXT] + + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb index a6ab83c9a7..1d1ef64120 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb @@ -21,7 +21,7 @@ dependencies = [ # recompile patch Cython source file prebuildopts = "cython scipy/linalg/_decomp_update.pyx && " -# need to use pip rather than regular 'setup.py install,' +# need to use pip rather than regular 'setup.py install' # to ensure that this scipy wins over the one in the Python installation; # using easy_install does not work... use_pip = True diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb index 39c950b357..a9245a0b76 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb @@ -5,8 +5,8 @@ easyblock = 'MakeCp' -name = "segemehl" -version = "0.2.0" +name = 'segemehl' +version = '0.2.0' homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' description = """ segemehl is a software to map short sequencer reads to reference genomes. @@ -20,7 +20,7 @@ description = """ segemehl is a software to map short sequencer reads to referen toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] -sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] +sources = ['%s_%s.tar.gz' % (name, version.replace('.', '_'))] parallel = 1 @@ -29,11 +29,11 @@ dependencies = [ ('zlib', '1.2.8'), ] -files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] +files_to_copy = [(['lack.x', 'segemehl.x', 'testrealign.x'], 'bin')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], - 'dirs': ["."] + 'files': ['bin/%s' % x for x in ['lack.x', 'segemehl.x', 'testrealign.x']], + 'dirs': [] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb index 241a1d5fbf..7c1426364f 100644 --- a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb @@ -4,7 +4,7 @@ name = "stemming" version = "1.0" homepage = "https://pypi.python.org/pypi/stemming/" -description = """Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English.""" +description = "Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English." toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb index 6ab91f87e3..1ee4a4a0bc 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -#Patch to fix tests +# patch to fix tests patches = ['sympy-1.0_tests-unicode.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb index 09140f6d09..1c13652bc7 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -#Patch to fix tests +# patch to fix tests patches = ['sympy-1.0_tests-unicode.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb index 2f2888a832..72a246892c 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb @@ -25,8 +25,8 @@ dependencies = [ ('PDT', '3.19'), ('Score-P', '1.2.1'), # obsolete backends, use Score-P instead - #('Scalasca', '1.4.3'), - #('VampirTrace', '5.14.4'), + # ('Scalasca', '1.4.3'), + # ('VampirTrace', '5.14.4'), ] # scalasca and vampirtrace backends are deprecated diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb index 5f116c4b08..71643e32bd 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb @@ -29,7 +29,7 @@ dependencies = [ ('ant', '1.9.6', '-%s-%s' % (java, javaver), True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.6'), - ('ncurses', '5.9',), + ('ncurses', '5.9'), ('zlib', '1.2.8'), ('Perl', '5.20.3'), ] diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index 58018d9335..181142b3db 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -30,7 +30,7 @@ dependencies = [ ('ant', '1.9.7', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), - ('ncurses', '6.0',), + ('ncurses', '6.0'), ('zlib', '1.2.8'), ('Perl', '5.22.1'), ] diff --git a/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb index ae04827ae1..ce865ad5b9 100644 --- a/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb @@ -22,9 +22,8 @@ USPEX can also be used for finding low-energy metastable phases, as well as stab toolchain = {'name': 'intel', 'version': '2016b'} +# you have to register before download via http://uspex-team.org/uspex/downloads sources = ['%(name)s-%(version)s.tar.gz'] -#You have to register before download -#source_urls = ['http://uspex-team.org/uspex/downloads'] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb index 933c8b66d8..3b7e3d4f5d 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('xcb-util', '0.4.0',), + ('xcb-util', '0.4.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb index 2e2077d599..f85c7f00dd 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums=['1fb2595d2a905a9e820c976a1d8348bc'] +checksums = ['1fb2595d2a905a9e820c976a1d8348bc'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb index b5d9aa81e3..4c59674a12 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums=['1fb2595d2a905a9e820c976a1d8348bc'] +checksums = ['1fb2595d2a905a9e820c976a1d8348bc'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' -- GitLab From 87b347871ec03bfdb8474f406965cb522ebf9dfa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Feb 2017 21:08:32 +0100 Subject: [PATCH 283/818] more style fixes in easyconfigs --- .../s/SHORE/SHORE-0.9.3-foss-2016a.eb | 8 +++---- .../SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb | 8 +++---- .../SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb | 9 ++++---- .../SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb | 8 +++---- .../SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb | 8 +++---- .../s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb | 3 ++- .../s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb | 3 ++- .../s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-foss-2016a.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb | 3 ++- .../s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb | 3 ++- .../SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-foss-2015b.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-intel-2015b.eb | 3 ++- .../s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb | 2 +- .../s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-foss-2016a.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-intel-2015b.eb | 3 ++- .../SQLite-3.9.2-intel-2016.02-GCC-4.9.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-intel-2016a.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb | 3 ++- ...Lite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 ++- ...R-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb | 10 ++++----- .../s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb | 7 +++---- .../s/STAR/STAR-2.5.0a-goolf-1.4.10.eb | 7 +++---- .../s/STAR/STAR-2.5.1b-foss-2015b.eb | 9 ++++---- .../s/STAR/STAR-2.5.1b-goolf-1.4.10.eb | 9 ++++---- .../s/STAR/STAR-2.5.2a-foss-2016a.eb | 21 +++++++++---------- .../s/STAR/STAR-2.5.2a-goolf-1.7.20.eb | 21 +++++++++---------- .../s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb | 2 +- .../Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 2 +- .../s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb | 2 +- .../s/Serf/Serf-1.3.8-foss-2015a.eb | 4 ++-- 43 files changed, 117 insertions(+), 98 deletions(-) diff --git a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb index 189d1b413d..4078e01a54 100644 --- a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -15,10 +15,10 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '--with-mpi' dependencies = [ - ('XZ', '5.2.2'), - ('zlib', '1.2.8'), - ('GSL', '1.16'), # GSL 2.1 does not work. - ('Boost', '1.61.0'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), # GSL 2.1 does not work. + ('Boost', '1.61.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb index 3c14ae7d6c..e137f85d4d 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb @@ -3,10 +3,10 @@ version = "3.3-p1" versionsuffix = '-Python-2.7.3' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of -large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or -generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, -rectangular matrix, and to solve quadratic eigenvalue problems.""" +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb index 1b4c48aa91..e3ec9ea769 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb @@ -3,11 +3,10 @@ version = "3.3-p1" versionsuffix = '-Python-2.7.3' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of - large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or - generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, - rectangular matrix, and to solve quadratic eigenvalue problems.""" - +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb index 0f01678e28..fd3e7c3888 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -3,10 +3,10 @@ version = '3.5.3' versionsuffix = '-Python-2.7.9' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of - large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either - standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial - SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb index 775feb3837..351ac62d2c 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb @@ -3,10 +3,10 @@ version = '3.6.2' versionsuffix = '-Python-2.7.11' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of - large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either - standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial - SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb index 762b8d9995..4a20471e6d 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb index 3d66a9ad8c..9464d99616 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb index 0b67d316a2..380060ff3b 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb index 59be5269fa..59c5938c90 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '6.1.0')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb index 4df722877b..36cdd512d2 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb index ba3405a6f5..44b9de5758 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb index 435de49323..def70b5b62 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb index d38cf61101..cb84023340 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb @@ -37,7 +37,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb index 62c6f7b8b2..15a228e4cf 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb index 06b2583e36..0e3d5b0943 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb index 5708afcd84..3cdb5e9a31 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb index 11fc55a1b6..c9bee3d1d5 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 6a41f5863c..2b1f98a6ac 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb index e06537d494..86716967ff 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb index 17d369e530..70270519d3 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb index 26439e2d65..5c38e72b1a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb index 5d1c89464a..0a07713fbb 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -19,7 +19,7 @@ description = "SQLite: SQL Database Engine in a C Library" # eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb index 429cfc37d8..408f74829a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb index 51941069b6..5c92bc8136 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb index 47bee4f624..8902612f46 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb index 8d257ce664..4b9cea2422 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb index c1e564bfd6..d75861cbb6 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb index 79c1231084..177a74a0fb 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb index 3555a7ac4c..885ab346a9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb index a35ea6d281..46583c5246 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb index 4eb223b17f..c1a72bbbe4 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index e099c4dd67..68f9f01974 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb index 58fcb58c2d..c87beb9409 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb @@ -30,17 +30,17 @@ exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ ('Set::IntervalTree', '0.10', { - 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], + 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], }), ('DB_File', '1.835', { - 'source_tmpl': 'DB_File-1.835.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + 'source_tmpl': 'DB_File-1.835.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], }), ] modextrapaths = { - 'PATH': "", # add installation dir to PATH + 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' } diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb index b6190397ee..bc379c42eb 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb @@ -9,8 +9,7 @@ name = 'STAR' version = '2.5.0a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,7 +28,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb index ee25be84dd..9bf855263a 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb @@ -9,8 +9,7 @@ name = 'STAR' version = '2.5.0a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,7 +28,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb index 406fea6072..947c48d129 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb @@ -8,11 +8,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.1b' +version = '2.5.1b' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'openmp': True} @@ -21,7 +20,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -31,7 +30,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb index b04986c691..c67472aaa1 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb @@ -6,11 +6,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.1b' +version = '2.5.1b' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,7 +28,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb index 769bc0a35c..b5f453b8c8 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb @@ -9,11 +9,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.2a' +version = '2.5.2a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'openmp': True} @@ -22,7 +21,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -32,15 +31,15 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", + (["source/STAR", "source/STARlong"], "bin"), + "CHANGES.md", + "doc", + "extras", + "LICENSE", + "README.md", "RELEASEnotes.md" ] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb index fd35161f48..545af822d8 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb @@ -6,11 +6,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.2a' +version = '2.5.2a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,15 +28,15 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", + (["source/STAR", "source/STARlong"], "bin"), + "CHANGES.md", + "doc", + "extras", + "LICENSE", + "README.md", "RELEASEnotes.md" ] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb index b96f631d9c..352f9013ea 100644 --- a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'SUMATRA' version = '1.0.20' -homepage = "http://metabarcoding.org/sumatra" +homepage = 'http://metabarcoding.org/sumatra' description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index 031be8f553..2de8d75b11 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -10,7 +10,7 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] -source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] +source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s', 'download'] dependencies = [('Java', '1.7.0_79')] diff --git a/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb index 29459a5481..86ba1ed78f 100644 --- a/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb @@ -23,7 +23,7 @@ dependencies = [ files_to_copy = [(['SeqPrep'], 'bin'), ] parallel = 1 - + sanity_check_paths = { 'files': ['bin/SeqPrep'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index 987ce669c8..dd4add0a50 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -21,8 +21,8 @@ builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] dependencies = [ ('APR', '1.5.2'), ('APR-util', '1.5.4'), - # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From c49c34991d67d6c086933324d4c1533ae7063f73 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 22 Feb 2017 11:09:07 +1030 Subject: [PATCH 284/818] meRanTK-1.1.1b added --- .../easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb new file mode 100644 index 0000000000..25c303ad85 --- /dev/null +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Manuel Sepulveda Escobedo +# License:: +# +# Notes:: +## + +name = 'meRanTK' +version = '1.1.1b' + +easyblock = 'BinariesTarball' +homepage = 'http://www.icbi.at/index.html' +description = """meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.icbi.at/software/meRanTK/downloads'] +sources = ['%s/meRanTK-%s.zip' %(version,version,)] + +dependencies = [ +] + +sanity_check_paths = { + 'files':['bin/meRanAnnotate'], + 'files':['bin/meRanCall'], + 'files':['bin/meRanCompare'], + 'files':['bin/meRanGs'], + 'files':['bin/meRanGt'], + 'files':['bin/meRanT'], + 'dirs':[], +} + +moduleclass = 'bio' -- GitLab From 3403881a052f5c7f80732205b069295dae319e9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 09:44:06 +0100 Subject: [PATCH 285/818] fix broken test in Cantera 2.3.0 rather than skipping it --- ...Cantera-2.3.0-intel-2016b-Python-2.7.12.eb | 2 +- .../Cantera-2.3.0_fix-test-reprod.patch | 31 +++++++++++++++++++ .../Cantera-2.3.0_skip-broken-tests.patch | 25 --------------- 3 files changed, 32 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch delete mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb index 594203f790..62c745b353 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'Cantera-%(version)s_fix-bug-416.patch', - 'Cantera-%(version)s_skip-broken-tests.patch', + 'Cantera-%(version)s_fix-test-reprod.patch', ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch new file mode 100644 index 0000000000..83dde312f8 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch @@ -0,0 +1,31 @@ +see https://github.com/Cantera/cantera/issues/433 and https://github.com/Cantera/cantera/commit/11a0727d5ca6172fcb3596dbc11e7f7b1cc2e806 + +From 11a0727d5ca6172fcb3596dbc11e7f7b1cc2e806 Mon Sep 17 00:00:00 2001 +From: Ray Speth +Date: Tue, 21 Feb 2017 20:29:37 -0500 +Subject: [PATCH] [Test] Fix reproducibility of values used in + add_species_sequential test + +Exact floating point equality can be assured only in the case where the species +are added in the same order, since this affects summations involved in +calculating the mixture molecular weight. This resulted in test failures with +certain versions of the Intel compiler. + +Resolves #433. +--- + test/data/kineticsfromscratch.cti | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/data/kineticsfromscratch.cti b/test/data/kineticsfromscratch.cti +index eaba17b..25983cf 100644 +--- a/test/data/kineticsfromscratch.cti ++++ b/test/data/kineticsfromscratch.cti +@@ -2,7 +2,7 @@ units(length='m', time='s', quantity='kmol', act_energy='cal/mol') + + ideal_gas(name = "ohmech", + elements = " O H Ar ", +- species = """ h2o2: H2 H O O2 OH H2O HO2 H2O2 AR""", ++ species = """ h2o2: AR O H2 H OH O2 H2O H2O2 HO2""", + reactions = "all", + transport = "None", + initial_state = state(temperature = 300.0, diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch deleted file mode 100644 index d3b26cf18f..0000000000 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch +++ /dev/null @@ -1,25 +0,0 @@ -skip broken test, fails due to strict floating-point value comparison -see https://github.com/Cantera/cantera/issues/433 - -author: Kenneth Hoste (HPC-UGent) - ---- test/kinetics/kineticsFromScratch.cpp.orig 2017-02-15 16:32:24.518921570 +0100 -+++ test/kinetics/kineticsFromScratch.cpp 2017-02-15 16:32:38.509147212 +0100 -@@ -453,7 +453,7 @@ - } - }; - --TEST_F(KineticsAddSpecies, add_species_sequential) -+/*TEST_F(KineticsAddSpecies, add_species_sequential) - { - ASSERT_EQ((size_t) 0, kin.nReactions()); - -@@ -480,7 +480,7 @@ - p.addSpecies(species["HO2"]); - kin.addReaction(reactions[4]); - check_rates(5, "O:0.01, H2:0.1, H:0.02, OH:0.03, O2:0.4, AR:0.3, H2O2:0.03, HO2:0.01"); --} -+}*/ - - TEST_F(KineticsAddSpecies, add_species_err_first) - { -- GitLab From c37616e94582207c44ea75ea166b7e4f96b664ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 10:34:28 +0100 Subject: [PATCH 286/818] adding easyconfigs: meshio-1.7.1-intel-2016b-Python-2.7.12.eb --- .../meshio-1.7.1-intel-2016b-Python-2.7.12.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d41f8720e8 --- /dev/null +++ b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'meshio' +version = '1.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nschloe/meshio' +description = "meshio is a tool for reading/writing various mesh formats representing unstructured meshes" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), # includes numpy + ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.18'), + ('VTK', '6.3.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('appdirs', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('pipdated', '0.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pipdated'], + }), +] + +sanity_check_paths = { + 'files': ['bin/meshio-convert'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'cae' -- GitLab From f1d9415b25a98b2b6668a260f91f83978a1a38fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 11:17:47 +0100 Subject: [PATCH 287/818] add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x --- .../x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 2 ++ .../x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 2 ++ .../XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 2 ++ .../XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 2 ++ .../x/XZ/XZ-5.2.2_compat-libs.patch | 27 +++++++++++++++++++ 13 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb index 96695c9d5c..6c49a4458b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb index f08ddf7da4..001a737c6e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb index d4f3584da4..f5d80fe9e5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.4', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 90393732b9..08aad5d870 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016.04'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 52273a7c6b..deb8d13a10 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index 8985ebbf18..a0c7f313e0 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.6', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index aaea1f659f..e891d5536a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index 1b63e65341..4c118e934f 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), ('gettext', '0.18.2', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index 2cb7040caf..43117900f6 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.18.2', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index 9822949071..0e6f109230 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index bcd46743d2..fdf1453ac4 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.6', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index 95304a848d..85431b3d6e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch b/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch new file mode 100644 index 0000000000..3090e4e0ea --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch @@ -0,0 +1,27 @@ +include two 5.1.2aplha symbols that were included in XZ 5.1.2alpha which are required by the 'rpm' command on CentOS 7.x +see also https://github.com/hpcugent/easybuild-easyconfigs/issues/4036 +original patch: xz-5.2.2-compat-libs.patch, cfr. https://git.centos.org/patch/rpms!xz.git/3f035cee1da9f864609885e5ef2a1be77cd37eee + +--- src/liblzma/liblzma.map.orig 2015-09-29 12:57:36.000000000 +0200 ++++ src/liblzma/liblzma.map 2017-02-22 11:10:33.432868185 +0100 +@@ -95,7 +95,13 @@ + lzma_vli_size; + }; + +-XZ_5.2 { ++XZ_5.1.2alpha { ++global: ++ lzma_stream_encoder_mt; ++ lzma_stream_encoder_mt_memusage; ++} XZ_5.0; ++ ++XZ_5.2.2 { + global: + lzma_block_uncomp_encode; + lzma_cputhreads; +@@ -105,4 +111,4 @@ + + local: + *; +-} XZ_5.0; ++} XZ_5.1.2alpha; -- GitLab From 20aeb9694bf980ddff62a92f4dee8e4c83abec20 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 22 Feb 2017 12:46:14 +0100 Subject: [PATCH 288/818] adding easyconfigs: stress-1.0.4-goolf-1.7.20.eb --- .../s/stress/stress-1.0.4-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb b/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..e91ebd2437 --- /dev/null +++ b/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'stress' +version = '1.0.4' + +homepage = 'http://people.seas.harvard.edu/~apw/stress/' +description = """stress is a deliberately simple workload generator for POSIX systems. + It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system. + It is written in C, and is free software licensed under the GPLv2.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://people.seas.harvard.edu/~apw/stress/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +runtest = "check" + +sanity_check_paths = { + 'files': ['bin/stress'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 21638aa97e214095a6737e9ce6bad388d60d7c99 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Feb 2017 13:44:49 +0000 Subject: [PATCH 289/818] fixed patch descriptions, added EB autotools --- .../i/igraph/igraph-0.7.1-intel-2016b.eb | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index 53b27e3fc2..68c14b0bae 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -14,9 +14,17 @@ toolchainopts = {'pic': True} sources = ['igraph-%(version)s.tar.gz'] source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] -# Fix llapack and llblas when compiling with MKL -# Fix aclocal which is hard-coded to version 1.14 -patches = ['igraph-0.7.1-no-lapack-no-blas.patch', 'igraph-0.7.1-fix-aclocal-version.patch'] +builddependencies = [('Autotools', '20150215')] + +patches = [ + # Author: Maxime Boissonneault + # Remove explicit linking on -llapack and -llblas, which are not found when linking against MKL + 'igraph-%(version)s-no-lapack-no-blas.patch', + + # Author: Maxime Boissonneault + # Fix explicit version of aclocal (specified 1.14). Replaced with version 1.15 which corresponds to the 20150215 Autotools + 'igraph-%(version)s-fix-aclocal-version.patch' + ] # link against MKL rather than blas/lapack preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" -- GitLab From fd948a94153527552aaf7a620f48b6b3b7606de7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 15:06:26 +0100 Subject: [PATCH 290/818] adding easyconfigs: CGAL-4.9-intel-2016b-Python-2.7.12.eb, Qt5-5.8.0-intel-2016b.eb, Eigen-3.3.3-intel-2016b.eb --- .../CGAL-4.9-intel-2016b-Python-2.7.12.eb | 36 +++++++++++++++++++ .../e/Eigen/Eigen-3.3.3-intel-2016b.eb | 13 +++++++ .../q/Qt5/Qt5-5.8.0-intel-2016b.eb | 33 +++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1e392edbad --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb new file mode 100644 index 0000000000..fdeb038ac8 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb new file mode 100644 index 0000000000..a05afd5096 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.8.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['Qt5-5.7.1_fix-nan-inf.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From 025436aa2f38dd73c5b65a23d304108a04699be6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 15:38:04 +0100 Subject: [PATCH 291/818] also update $PATH in OrthoMCL 1.4 easyconfig --- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 6820502e94..55f6dee9e2 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -28,8 +28,14 @@ sanity_check_paths = { 'dirs': ['sample_data'], } -modextrapaths = {'PERL5LIB': ''} +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} -sanity_check_commands = [('perl', '-e "use orthomcl_module;"')] +sanity_check_commands = [ + "orthomcl.pl --help 2>&1 | grep Usage", + "perl -e 'use orthomcl_module;'", +] moduleclass = 'bio' -- GitLab From 8eb3821e5f0dd65e74a6bdb6d9d8db6d4b28ea71 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 16:27:20 +0000 Subject: [PATCH 292/818] Changed to intel,2017a toolchain --- .../b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb new file mode 100644 index 0000000000..e573ab735a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -0,0 +1,20 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['int64typedef.patch','void2int.patch'] + +moduleclass = 'bio' -- GitLab From 29d274f5ae6614213f1f0fb1db0d873782922e78 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 17:07:17 +0000 Subject: [PATCH 293/818] delete Bowtie-1.1.2-iimkl-2017a.eb --- .../b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb deleted file mode 100644 index 500679eb6f..0000000000 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb +++ /dev/null @@ -1,20 +0,0 @@ -# Modified from existing version by: -# Robert Schmidt -# Ottawa Hospital Research Institute - Bioinformatics Team -name = 'Bowtie' -version = '1.1.2' - -homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' -description = """Bowtie is an ultrafast, memory-efficient short read aligner. -It aligns short DNA sequences (reads) to the human genome. -""" - -toolchain = {'name': 'iimkl', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://download.sourceforge.net/bowtie-bio/'] - -patches = ['int64typedef.patch','void2int.patch'] - -moduleclass = 'bio' -- GitLab From 8566fc7e05fb81386d3b2684d19ee4d523197b3f Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 17:22:28 +0000 Subject: [PATCH 294/818] Added comments to void2int.patch --- easybuild/easyconfigs/b/Bowtie/void2int.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie/void2int.patch b/easybuild/easyconfigs/b/Bowtie/void2int.patch index 80b76591d4..b2b7d467a3 100644 --- a/easybuild/easyconfigs/b/Bowtie/void2int.patch +++ b/easybuild/easyconfigs/b/Bowtie/void2int.patch @@ -1,3 +1,6 @@ +#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument +#being incompatible with parameter of type "int *" +#M. Fujinaga (fujinaga@ualberta.ca) --- processor_support.h.orig 2017-02-02 21:48:42.436432756 +0000 +++ processor_support.h 2017-02-02 21:48:54.419309743 +0000 @@ -44,8 +44,8 @@ -- GitLab From 646b59d0a5b6ad6be3619c1b2c8f519a7f7cff7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 18:51:23 +0100 Subject: [PATCH 295/818] fix hardcoded paths in OrthoMCL 1.4 installation --- .../OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 55f6dee9e2..8cdb56fbdb 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -19,20 +19,30 @@ dependencies = [ ('Perl', '5.24.0'), ('MCL', '%s.%s' % (mcl_majver, mcl_minver)), ('BioPerl', '1.7.1', versionsuffix), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ] start_dir = 'ORTHOMCLV%(version)s' -sanity_check_paths = { - 'files': ['orthomcl_module.pm', 'orthomcl.pl', 'README'], - 'dirs': ['sample_data'], -} +# fix hardcoded paths +postinstallcmds = [ + 'sed -i"" "s@/usr/bin/perl@$EBROOTPERL/bin/perl@g" %(installdir)s/orthomcl.pl', + 'sed -i"" "s@\\"/.*blastall\\";@\\"$EBROOTBLAST/bin/blastall\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@\\"/.*formatdb\\";@\\"$EBROOTBLAST/bin/formatdb\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@\\"/.*mcl\\";@\\"$EBROOTMCL/bin/mcl\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@\\"/.*ORTHOMCL.*%(version)s/\\";@\\"\\$ENV{\'PWD\'}/\\";@g" %(installdir)s/orthomcl_module.pm', +] modextrapaths = { 'PATH': '', 'PERL5LIB': '', } +sanity_check_paths = { + 'files': ['orthomcl_module.pm', 'orthomcl.pl', 'README'], + 'dirs': ['sample_data'], +} + sanity_check_commands = [ "orthomcl.pl --help 2>&1 | grep Usage", "perl -e 'use orthomcl_module;'", -- GitLab From 45166cf524156762318bcb5e1742c503bc032662 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:07:17 +0100 Subject: [PATCH 296/818] adding easyconfigs: matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb --- .../f/freetype/freetype-2.7.1-intel-2016b.eb | 26 +++++++++++ .../l/libpng/libpng-1.6.27-intel-2016b.eb | 26 +++++++++++ ...plotlib-2.0.0-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb new file mode 100644 index 0000000000..d3a160563e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.27'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb new file mode 100644 index 0000000000..e0204f6881 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.27' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..def79919ce --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.7.1'), + ('libpng', '1.6.27'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From e068d3f6eef6a902f63a06ec7485472d1b1347e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:12:06 +0100 Subject: [PATCH 297/818] adding easyconfigs: IPython-5.2.2-intel-2016b-Python-2.7.12.eb --- ...IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 151 ++++++++++++++++++ .../path.py-10.1-intel-2016b-Python-2.7.12.eb | 30 ++++ ...oolkit-1.0.13-intel-2016b-Python-2.7.12.eb | 30 ++++ 3 files changed, 211 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bc8f42751d --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,151 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('Python', '2.7.12'), + ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), + # required by 'nbconvert', but causes problems w.r.t. 'backports' module... + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('entrypoints', '0.2.2', versionsuffix), + ('path.py', '10.1', versionsuffix), + ('prompt-toolkit', '1.0.13', versionsuffix), +] + +# this is a bundle of Python packages +# XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have +# to be included as dependencies because bundling wheels does not work +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2017.1.23', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.9.5', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + # disabled because entrypoints on which this depends pull in configparser, which causes problems + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('nbconvert', '5.1.1', { + # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + #}), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), + ('ipywidgets', '5.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '1.2.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d128f00a07 --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'path.py' +version = '10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaraco/path.py' +description = """path.py is a Python library implementing path objects as first-class entities, + allowing common operations on files to be invoked on those path objects directly.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0dc0fbea27 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = ['prompt_toolkit-%(version)s-py2-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('wcwidth', '0.1.7', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' -- GitLab From 7ab0d656dd4fd3170d0b197481127c1d36f2c4a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:13:07 +0100 Subject: [PATCH 298/818] adding easyconfigs: VTK-7.1.0-intel-2016b-Python-2.7.12.eb --- .../VTK-7.1.0-intel-2016b-Python-2.7.12.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ff2f4a0f63 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,58 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '7.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.7.2')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From 4b9994f8d76853810b7b36a486c27c2dd76704e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:15:10 +0100 Subject: [PATCH 299/818] adding easyconfigs: Yade-2017.01a-intel-2016b-Python-2.7.12.eb, libQGLViewer-2.6.4-intel-2016b.eb, minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb --- .../libQGLViewer-2.6.4-intel-2016b.eb | 20 ++++++ ...-intel-2016b-Python-2.7.12-Boost-1.63.0.eb | 27 ++++++++ ...Yade-2017.01a-intel-2016b-Python-2.7.12.eb | 61 +++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb create mode 100644 easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb new file mode 100644 index 0000000000..b66d7bd768 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb @@ -0,0 +1,20 @@ +name = 'libQGLViewer' +version = '2.6.4' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libGLU', '9.0.0'), +] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb new file mode 100644 index 0000000000..4226d4a6e1 --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +boostver = '1.63.0' +versionsuffix = '-Python-%%(pyver)s-Boost-%s' % boostver + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', boostver, '-Python-%(pyver)s'), + ('Eigen', '3.3.3'), + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5f79b0294c --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,61 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '2017.01a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('CGAL', '4.9', versionsuffix), + ('GDB', '7.11.1', versionsuffix), + ('GL2PS', '1.3.9'), + ('GTS', '0.7.6'), + ('IPython', '5.2.2', versionsuffix), + ('libQGLViewer', '2.6.4'), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.2', versionsuffix), + ('minieigen', '0.5.3', versionsuffix + '-Boost-1.63.0'), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.12'), + ('Qt5', '5.8.0'), + ('SQLite', '3.13.0'), + ('VTK', '7.1.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' % SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From dfe6c82f37987b616023f96006e0daec02f9aa83 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 18:41:24 +0000 Subject: [PATCH 300/818] Stylistic changes --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 7 +++++-- .../Bowtie/{void2int.patch => Bowtie-1.1.2_void2int.patch} | 0 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/b/Bowtie/{void2int.patch => Bowtie-1.1.2_void2int.patch} (100%) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb index e573ab735a..db4bf02c9f 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -10,11 +10,14 @@ It aligns short DNA sequences (reads) to the human genome. """ toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] -patches = ['int64typedef.patch','void2int.patch'] +patches = [ + 'int64typedef.patch', + 'void2int.patch' +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/void2int.patch b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch similarity index 100% rename from easybuild/easyconfigs/b/Bowtie/void2int.patch rename to easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch -- GitLab From 1a3cdba55d30d08a8a83ffbc4c2c28af55589525 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:43:12 +0100 Subject: [PATCH 301/818] bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a --- .../m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb index d41f8720e8..cda151feb8 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), # includes numpy ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.18'), - ('VTK', '6.3.0', versionsuffix), + ('VTK', '7.1.0', versionsuffix), ] exts_defaultclass = 'PythonPackage' -- GitLab From 4ac20d4004c8e89e3659ce635ac7a8275231c4e9 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 19:01:17 +0000 Subject: [PATCH 302/818] Correct patch file name in easyconfig --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb index db4bf02c9f..2f5b9aef33 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -17,7 +17,7 @@ source_urls = ['http://download.sourceforge.net/bowtie-bio/'] patches = [ 'int64typedef.patch', - 'void2int.patch' + 'Bowtie-%(version)_void2int.patch' ] moduleclass = 'bio' -- GitLab From 764c127d8474caf90fd492d65653aed6b910fe94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 20:02:33 +0100 Subject: [PATCH 303/818] fix remarks --- .../easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb | 9 ++------- easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb | 9 ++------- easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb | 5 +++-- 7 files changed, 23 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb index bc379c42eb..04188b3f1a 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb @@ -27,7 +27,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb index 9bf855263a..457ab933f7 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb @@ -27,7 +27,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb index 947c48d129..b4f28e006e 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb @@ -29,7 +29,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb index c67472aaa1..acf5436cbe 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb @@ -27,7 +27,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb index b5f453b8c8..43cc47b2aa 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb @@ -31,13 +31,8 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", - "RELEASEnotes.md" + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb index 545af822d8..d8c6f0be04 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb @@ -28,13 +28,8 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", - "RELEASEnotes.md" + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index dd4add0a50..2852bb52f5 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -21,8 +21,9 @@ builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] dependencies = [ ('APR', '1.5.2'), ('APR-util', '1.5.4'), - # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From 11f27f266a4522fccc531926731e2b381ac4f235 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 19:07:01 +0000 Subject: [PATCH 304/818] second correction of easyconfig --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb index 2f5b9aef33..a59e6f69ac 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -17,7 +17,7 @@ source_urls = ['http://download.sourceforge.net/bowtie-bio/'] patches = [ 'int64typedef.patch', - 'Bowtie-%(version)_void2int.patch' + 'Bowtie-%(version)s_void2int.patch' ] moduleclass = 'bio' -- GitLab From 7800a4e5451a7ebaed4e93fa4dd64415f2ea7142 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Feb 2017 20:03:38 +0000 Subject: [PATCH 305/818] Added comments in the patch --- .../i/igraph/igraph-0.7.1-fix-aclocal-version.patch | 6 ++++++ .../i/igraph/igraph-0.7.1-no-lapack-no-blas.patch | 5 +++++ 2 files changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch index fc7ded594f..81b9d69187 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch @@ -1,3 +1,9 @@ +Change the version of autoconf which is required to configure from 1.14 to 1.15 + +From: Maxime Boissonneault +Date: Wed, 22 Feb 2017 + + diff -ru igraph-0.7.1.orig/aclocal.m4 igraph-0.7.1/aclocal.m4 --- igraph-0.7.1.orig/aclocal.m4 2014-04-22 17:54:54.000000000 +0000 +++ igraph-0.7.1/aclocal.m4 2017-02-21 15:10:50.062279982 +0000 diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch index 70635982cf..339e68cee3 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch @@ -1,3 +1,8 @@ +Removes explicit linking of libblas and liblapack for when linking with MKL + +From: Maxime Boissonneault +Date: Wed, 22 Feb 2017 + diff -ru igraph-0.7.1.orig/configure igraph-0.7.1/configure --- igraph-0.7.1.orig/configure 2014-04-22 17:55:00.000000000 +0000 +++ igraph-0.7.1/configure 2017-02-21 15:00:00.398921297 +0000 -- GitLab From eb544d54e03bef5fc962f1c76c127517e7765a00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 21:29:48 +0100 Subject: [PATCH 306/818] clean up trailing whitespace --- .../a/ant/ant-1.10.0-Java-1.8.0_112.eb | 2 +- .../a/ant/ant-1.9.7-Java-1.8.0_92.eb | 2 +- ...ommet-20150415-foss-2016a-Python-2.7.11.eb | 22 +++++----- ...cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 2 +- .../GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb | 2 +- .../GMAP-GSNAP-2016-05-01-foss-2016a.eb | 2 +- .../GMAP-GSNAP-2016-11-07-foss-2016b.eb | 2 +- .../g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb | 4 +- .../easyconfigs/g/gompi/gompi-2016.09.eb | 36 +++++++-------- .../g/grabix/grabix-0.1.6-goolf-1.7.20.eb | 6 +-- .../h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb | 44 +++++++++---------- .../h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb | 44 +++++++++---------- .../h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb | 44 +++++++++---------- .../i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb | 8 ++-- .../Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb | 4 +- .../m/Mono/Mono-2.10.6-intel-2016b.eb | 2 +- .../m/Mono/Mono-4.6.2.7-intel-2016b.eb | 2 +- easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb | 2 +- .../networkx-1.11-foss-2016a-Python-2.7.11.eb | 2 +- .../networkx-1.11-foss-2016a-Python-3.5.1.eb | 2 +- .../numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb | 40 ++++++++--------- .../numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb | 40 ++++++++--------- .../p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb | 2 +- .../PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 2 +- .../p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb | 2 +- .../SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb | 6 +-- 26 files changed, 163 insertions(+), 163 deletions(-) diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb index cf1f192a70..2d88d28b75 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -1,6 +1,6 @@ name = 'ant' version = '1.10.0' -versionsuffix = '-Java-%(javaver)s' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb index 186bcfb543..175bb2628a 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb @@ -1,6 +1,6 @@ name = 'ant' version = '1.9.7' -versionsuffix = '-Java-%(javaver)s' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index a2bd44831e..3abe5c93c9 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -1,27 +1,27 @@ -easyblock = 'MakeCp' +easyblock = 'MakeCp' -name = 'Commet' -version = '20150415' +name = 'Commet' +version = '20150415' commit = '4ef0705' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' -homepage = 'https://colibread.inria.fr/software/commet/' +homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of - a large metagenomic project. -""" + a large metagenomic project. +""" toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/pierrepeterlongo/commet/archive'] sources = ['%s.tar.gz' % commit] -checksums = ['19cba09ca7a92eaed75ed6af820d9451'] +checksums = ['19cba09ca7a92eaed75ed6af820d9451'] dependencies = [ - ('Python', '2.7.11'), -] + ('Python', '2.7.11'), +] -files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] +files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 5c57e5846c..99d5dfa45c 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,7 @@ easyblock = "PythonPackage" name = 'cutadapt' version = '1.9.1' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb index db19b2803a..5440f25394 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = "2015-12-31.v2" diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index 84e054bf9c..5e9cfedc47 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = '2016-05-01' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb index a8ca27958e..00035603e7 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb @@ -6,7 +6,7 @@ # Adam Huffman # The Francis Crick Institute -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = '2016-11-07' diff --git a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb index e78f2ba765..f302d9f398 100644 --- a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GP2C' version = '0.0.9pl5' -homepage = 'http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html' +homepage = 'http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html' description = """The gp2c compiler is a package for translating GP routines into the C programming language, so that they can be compiled and used with the PARI system or the GP calculator. """ @@ -17,7 +17,7 @@ dependencies = [ ('PARI-GP', '2.7.6'), ] -configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' +configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' runtest = 'check' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb index b4350de73a..d4b83fb9a0 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -1,20 +1,20 @@ -easyblock = "Toolchain" +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.09' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, +including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.2.0-2.27' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC and binutils + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), +] -name = 'gompi' -version = '2016.09' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, -including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -gccver = '6.2.0-2.27' - -# compiler toolchain dependencies -dependencies = [ - ('GCC', gccver), # includes both GCC and binutils - ('OpenMPI', '2.0.1', '', ('GCC', gccver)), -] - moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb index fc1bd33358..1bf0222ad3 100644 --- a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'grabix' -version = '0.1.6' +version = '0.1.6' homepage = 'https://github.com/arq5x/grabix' description = """a wee tool for random access into BGZF files""" @@ -17,13 +17,13 @@ source_urls = ['https://github.com/arq5x/grabix/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] parallel = 1 files_to_copy = [(["grabix"], "bin"), "README.md", "tests", "test.sh"] - + sanity_check_paths = { 'files': ["bin/grabix"], 'dirs': [], diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb index 35ced3699b..071326cd0d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.4' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb index a83862d853..ed51d67326 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.4' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'gcccuda', 'version': '2016.10'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'gcccuda', 'version': '2016.10'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb index b130fe6456..1aeec6a116 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.5' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb index 521eb6e805..1c64db33bd 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb @@ -6,10 +6,10 @@ easyblock = 'ConfigureMake' name = "IOR" -version = "3.0.1" +version = "3.0.1" versionsuffix = "-mpiio" -homepage = 'https://github.com/chaos/ior' +homepage = 'https://github.com/chaos/ior' description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. """ @@ -18,7 +18,7 @@ toolchain = {'name': 'foss', 'version': '2016a' } source_urls = [('https://github.com/chaos/ior/archive/')] sources = ['%(version)s.tar.gz'] -# configure opts listed below +# configure opts listed below # --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] # --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) # --with-lustre support configurable Lustre striping values [default=check] @@ -26,7 +26,7 @@ sources = ['%(version)s.tar.gz'] # --with-mpiio support IO with MPI-IO backend [default=yes] # --with-hdf5 support IO with HDF5 backend [default=no] # --with-ncmpi support IO with NCMPI backend [default=no] -preconfigopts = "./bootstrap &&" +preconfigopts = "./bootstrap &&" sanity_check_paths = { 'files': ["bin/ior"], diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb index 7235621e5d..5b5a91c678 100644 --- a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -1,13 +1,13 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'ConfigureMake' name = 'Mawk' version = '1.3.4' -versionsuffix = '-20150503' +versionsuffix = '-20150503' homepage = 'http://invisible-island.net/mawk/' description = """mawk is an interpreter for the AWK Programming Language.""" diff --git a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb index 365455df1b..e8b59e1494 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'Mono' version = '2.10.6' -homepage = 'http://mono-framework.com' +homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb index 4b58a5cd71..11e5afa9ee 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'Mono' version = '4.6.2.7' -homepage = 'http://mono-framework.com' +homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb index ea1fdc2813..5d4a7d1a7d 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb @@ -1,7 +1,7 @@ name = 'Mono' version = '4.6.2.7' -homepage = 'http://mono-framework.com' +homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb index 8dde76eb25..afc809e585 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'networkx' version = '1.11' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb index 488dd6f650..162c58702c 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'networkx' version = '1.11' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb index 7d6ccf3999..01a8bfdf0f 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.11' - -homepage = 'http://oss.sgi.com/projects/libnuma/' -description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. -It does this by supplying a NUMA memory policy to the operating system before running your program. -The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" - +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} -source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] -sources = [SOURCE_TAR_GZ] - -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb index ee922f3337..7fe4d082b3 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.11' - -homepage = 'http://oss.sgi.com/projects/libnuma/' -description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. -It does this by supplying a NUMA memory policy to the operating system before running your program. -The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" - +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} -source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] -sources = [SOURCE_TAR_GZ] - -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb index c67cbf7de9..807e673a1f 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PARI-GP' version = '2.7.6' -homepage = 'http://pari.math.u-bordeaux.fr' +homepage = 'http://pari.math.u-bordeaux.fr' description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index 61cae6188e..6d4327f5c0 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -4,7 +4,7 @@ name = 'PLAST' version = '2.3.1' versionsuffix = '-Java-%(javaver)s' -homepage = "http://www.irisa.fr/symbiose/projects/plast/" +homepage = "http://www.irisa.fr/symbiose/projects/plast/" description = """PLAST is a parallel alignment search tool for comparing large protein banks""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb index 7dffcdb458..fb465f5c89 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'Platanus' -version = '1.2.4' +version = '1.2.4' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" diff --git a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb index a2a47d4c1e..bbf5a698d9 100644 --- a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb @@ -1,13 +1,13 @@ # Author: Pablo Escobar Lopez; Wiktor Jurkowski # Swiss Institute of Bioinformatics (SIB), Biozentrum - University of Basel -# Babraham Institute, UK +# Babraham Institute, UK easyblock = 'MakeCp' name = 'SUMACLUST' version = '1.0.20' -homepage = "http://metabarcoding.org/sumatra" +homepage = "http://metabarcoding.org/sumatra" description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/'] sources = ['%(namelower)s_v%(version)s.tar.gz'] -prebuildopts = 'make clean &&' +prebuildopts = 'make clean &&' files_to_copy = [(['sumaclust'], 'bin'), 'sumaclust_user_manual.pdf'] -- GitLab From 5e41c7e7ff395d5f331dfcfda505bc47d13f8df8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 21:35:28 +0100 Subject: [PATCH 307/818] remove whitespace from blank lines --- easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb | 2 +- .../easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb | 4 ++-- .../easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb | 6 +++--- .../easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb | 8 ++++---- .../easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb | 4 ++-- ...fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb | 8 ++++---- .../g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb | 2 +- .../MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb | 6 +++--- .../m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb | 6 +++--- easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb | 4 ++-- .../QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 8 ++++---- .../easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb | 6 +++--- 13 files changed, 34 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb index c9d9db6e85..39352e91cb 100644 --- a/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb +++ b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb @@ -5,7 +5,7 @@ version = '0.910' homepage = 'http://www.popgen.dk/angsd' description = """Program for analysing NGS data.""" - + toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/ANGSD/angsd/archive/'] diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb index cd1dd2595a..25707a1810 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -23,7 +23,7 @@ start_dir = 'source' files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescenv'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb index 7a976185d2..25b2cd8bb7 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -22,7 +22,7 @@ start_dir = 'source' files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescenv'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index c4932d3953..ebd814c54e 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -9,7 +9,7 @@ name = 'BayeScan' version = '2.1' homepage = 'http://cmpg.unibe.ch/software/BayeScan/' -description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -30,7 +30,7 @@ files_to_copy = [ ] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescan_%(version)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb index 3745f65f5f..de8bcce297 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -9,10 +9,10 @@ name = 'BayeScan' version = '2.1' homepage = 'http://cmpg.unibe.ch/software/BayeScan/' -description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" -# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile +# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -31,7 +31,7 @@ files_to_copy = [ 'R functions'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescan_%(version)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index 7a15e698bd..8c2ecba76b 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -27,7 +27,7 @@ prebuildopts += ' ../configure --enable-static --disable-debug --enable-optimisa files_to_copy = [(['build/ctffind'], 'bin'), 'doc', 'scripts'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/ctffind'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb index 7eeaa4c1a4..f9d3b4a7b5 100644 --- a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb +++ b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -20,12 +20,12 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} # using latest release tags doesn't work # https://github.com/statgen/fastQValidator/issues/9 source_urls = [ - 'https://github.com/statgen/fastQValidator/archive/', + 'https://github.com/statgen/fastQValidator/archive/', 'https://github.com/statgen/libStatGen/archive/' ] sources = [ - '%s.tar.gz' % fastqvalidator_git_commit, + '%s.tar.gz' % fastqvalidator_git_commit, '%s.tar.gz' % libstatgen_git_commit ] @@ -46,7 +46,7 @@ buildopts = ' LIB_PATH_GENERAL=../libStatGen ' files_to_copy = [(['bin/fastQValidator'], 'bin')] parallel = 1 - + sanity_check_paths = { 'files': ['bin/fastQValidator'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb index 3053b75ee0..acdde9dd04 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb @@ -18,7 +18,7 @@ versionsuffix = '-Python-%s' % pyver dependencies = [('Python', pyver)] builddependencies = [('SWIG', '3.0.8', versionsuffix)] - + configopts = '--enable-python' modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb index 5b23296323..4a0d2c666a 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -11,7 +11,7 @@ git_commit_id = '24cf06' #first six digits of the commit id we will download fro versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' -description = """ MOSAIK is a reference-guided aligner for next-generation +description = """ MOSAIK is a reference-guided aligner for next-generation sequencing technologies """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -28,7 +28,7 @@ start_dir = "src" buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] - + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], 'dirs': [], diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb index 77047640bf..06031fc9f0 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -11,7 +11,7 @@ git_commit_id = '24cf06' #first six digits of the commit id we will download fro versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' -description = """ MOSAIK is a reference-guided aligner for next-generation +description = """ MOSAIK is a reference-guided aligner for next-generation sequencing technologies """ toolchain = {'name': 'ictce', 'version': '6.2.5'} @@ -28,7 +28,7 @@ start_dir = "src" buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] - + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], 'dirs': [], diff --git a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb index 59517cb978..86cd994610 100644 --- a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb @@ -6,7 +6,7 @@ version = '0.6.5' homepage = 'https://github.com/lh3/psmc' description = """This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.""" - + toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/lh3/psmc/archive/'] @@ -16,7 +16,7 @@ buildopts = '&& cd utils && make' utils = [ 'avg.pl', 'calD', 'cntcpg', 'ctime_plot.pl', 'dec2ctime.pl', 'decode2bed.pl', 'fq2psmcfa', 'history2ms.pl', - 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', + 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', ] files_to_copy = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 57849d2efa..b1b7c57728 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -11,7 +11,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True, 'openmp': True} -# this list was determined from QE 5.4.0 version release +# this list was determined from QE 5.4.0 version release sources = [ # Common source 'espresso-%(version)s.tar.gz', @@ -32,7 +32,7 @@ source_urls = [ 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz # These will not be used because of the 404 signal not found from the previous link. 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz @@ -46,8 +46,8 @@ source_urls = [ # Hybrid option exists only for backward compatibility, use toolchain option openmp instead. hybrid = True # Patch file to avoid the CPP problem generated by different OSes -patches = ['QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch'] - +patches = ['QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch'] + # packages included in 5.4.0 version of QE. We met errors when try to include gipaw, yambo and someother packages. buildopts = 'all tddfpt neb xspectra ph ' diff --git a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb index e5d10e8061..ebe8bfa5d5 100644 --- a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -18,11 +18,11 @@ sources = ['%(name)s_%(version)s.tar.gz'] buildopts = ' CC=$CC' -files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', +files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] parallel = 1 - + sanity_check_paths = { 'files': ['bin/rainbow', 'bin/ezmsim', 'bin/rbasm'], 'dirs': [], -- GitLab From c69a2ada4ad62775620a7eee897e439ae28e0954 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 21:45:13 +0100 Subject: [PATCH 308/818] include two spaces before inline comment --- .../cclib-1.5-foss-2016b-Python-3.5.2.eb | 2 +- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb | 2 +- .../g/GCC/GCC-4.8.2-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 2 +- .../g/GCC/GCC-4.8.3-CLooG-multilib.eb | 2 +- .../g/GCC/GCC-4.8.4-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb | 2 +- .../g/GCC/GCC-4.9.0-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb | 2 +- .../g/GCC/GCC-4.9.1-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb | 2 +- .../g/GCC/GCC-4.9.2-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb | 2 +- .../g/GCC/GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 2 +- .../i/intelcuda/intelcuda-2016.10.eb | 2 +- ...AIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb | 2 +- ...SAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb | 2 +- ...J-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- ...Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 2 +- .../OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 2 +- .../OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb | 2 +- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb | 6 ++--- ...PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 6 ++--- .../PostgreSQL-9.3.5-intel-2014b.eb | 2 +- ...tgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 2 +- ...tgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 2 +- ...tgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb | 2 +- ...gres-XL-9.5r1-intel-2016a-Python-2.7.11.eb | 2 +- .../p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 2 +- .../p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 2 +- ...QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 22 +++++++++---------- .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 2 +- .../easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- .../easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 6 ++--- .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- .../easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 2 +- .../easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 2 +- .../easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 2 +- .../easyconfigs/r/Reads2snp/Reads2snp-2.0.eb | 2 +- 50 files changed, 66 insertions(+), 66 deletions(-) diff --git a/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb index 78196b3b89..fe63f8a29c 100644 --- a/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/cclib/cclib/releases/download/v%(version)s/'] sources = ['%(name)s-%(version)s.post1.tar.gz'] dependencies = [ - ('Python', '3.5.2'), # This contains numpy as extension needed for cclib + ('Python', '3.5.2'), # This contains numpy as extension needed for cclib ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 2c6c725788..4851fc5541 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -36,7 +36,7 @@ common_configopts += 'LIBS="$LIBSCALAPACK" ' configopts = [ common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. ] buildopts = ' V=1 ' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 041898fae9..618d553031 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 91e4497eaa..6d29040095 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index d6ce9a89a0..9a60bde46d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index a5d4cd082d..54f482d906 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index 1d2159779b..89f13931a3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index bcc4336300..1fee24d2ad 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index 1293532d23..c0cd444cef 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 82341a9a29..7a4b755a4c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index 7f03450a91..bd08517bfa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index 163de21ca1..5cb7dc788a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index 323622921d..4b52dcc343 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index b5769a1078..1ec5100100 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 4820fd1026..897ca9088c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -19,7 +19,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index f182579664..88c83fce42 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index 47b8d2c23b..4052ab789b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index 3aa9d513bb..30c9cc61c0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 4998bcfaba..508f91d3f8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 2a3fe7ab85..1a5cf8b884 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 603dbd6cc5..a645d60588 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ source_urls = [ 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'https://ftp.gnu.org/gnu/gcc/gcc-%(version)s/', # Alternative GCC - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 5b1200a09b..a460408c19 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index 725e558810..a581540c04 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index ac6a734e6e..82121910a8 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -16,7 +16,7 @@ gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) comp = (comp_name, '%s%s' % (comp_ver, gccsuff)) dependencies = [ - comp, # part of iimpic + comp, # part of iimpic ('CUDA', '8.0.44', '', comp), ('icc', comp_ver, gccsuff), ('ifort', comp_ver, gccsuff), diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb index 4a0d2c666a..a98288f900 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' -git_commit_id = '24cf06' #first six digits of the commit id we will download from github +git_commit_id = '24cf06' # first six digits of the commit id we will download from github versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb index 06031fc9f0..3ce4130b75 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' -git_commit_id = '24cf06' #first six digits of the commit id we will download from github +git_commit_id = '24cf06' # first six digits of the commit id we will download from github versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 3bb9c9fb71..21ae128381 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -36,7 +36,7 @@ modextrapaths = { } modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory } sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 8c2cfb12b9..41195e5042 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -39,7 +39,7 @@ modextrapaths = { } modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory } sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 3dfb0c023b..26ff9690ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index 274fb15e1f..64e4eca3c7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -15,7 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb index fd6bb36c38..f7b06dcb04 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -17,7 +17,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.4')] diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index 1d36878e90..c76887ac30 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -101,13 +101,13 @@ exts_list = [ sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] modextrapaths = { - 'PATH': "", # add installation dir to PATH + 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line - "chmod +x %(installdir)s/*.pl" # add execution permission + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index fc0341658f..4dc47a8df2 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -99,13 +99,13 @@ exts_list = [ sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] modextrapaths = { - 'PATH': "", # add installation dir to PATH + 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line - "chmod +x %(installdir)s/*.pl" # add execution permission + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 815c947eac..b694510474 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -27,7 +27,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index 9afa456cae..a7d2b6c4a0 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index fca7dea11c..46e78c9224 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb index a1b0d0ba13..8f8750717c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.12'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb index 01c5da8a48..8261dc989e 100644 --- a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb @@ -19,7 +19,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index 2c98486b92..a0d5fb01e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index 23449c0834..eb90e5f158 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index b1b7c57728..09b026a284 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -29,18 +29,18 @@ sources = [ ] source_urls = [ 'http://files.qe-forge.org/index.php?file=', # Almost all - 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz # These will not be used because of the 404 signal not found from the previous link. - 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz ] # Hybrid option exists only for backward compatibility, use toolchain option openmp instead. diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index b54b0f68e9..95846046fc 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.45.0'), # for RCurl ('libxml2', '2.9.2'), # for XML ('GDAL', '2.0.1'), # for rgdal - ('PROJ', '4.8.0'), # for rgdal + ('PROJ', '4.8.0'), # for rgdal ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 580f74438d..1389b272dd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.47.0'), # for RCurl ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.0'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index 004c178582..0acfcbd0b3 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 1a886a00c9..39a19900bb 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -28,15 +28,15 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('LibTIFF', '4.0.6'), # for plotting in R - ('cairo', '1.14.6'), # for plotting in R + ('LibTIFF', '4.0.6'), # for plotting in R + ('cairo', '1.14.6'), # for plotting in R ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.0'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 7baa761be0..ad907eaa04 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.47.0'), # for RCurl ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.0'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 7ed2007d87..7c7e501aad 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index e6d46c62ea..9380aadc9b 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -31,7 +31,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index 09f5b0a4c6..88223934d1 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -31,7 +31,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 506890dce2..462568a58d 100644 --- a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -25,7 +25,7 @@ sanity_check_paths = { } modextrapaths = { - 'PATH': "", # add the installation dir to PATH + 'PATH': "", # add the installation dir to PATH } moduleclass = 'bio' -- GitLab From 465017c088b49dcbf976764f7fe42a80326b9149 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Feb 2017 21:34:48 +0000 Subject: [PATCH 309/818] removed comments from the recipe --- easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index 68c14b0bae..ddf779e0e0 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -17,12 +17,7 @@ source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] builddependencies = [('Autotools', '20150215')] patches = [ - # Author: Maxime Boissonneault - # Remove explicit linking on -llapack and -llblas, which are not found when linking against MKL 'igraph-%(version)s-no-lapack-no-blas.patch', - - # Author: Maxime Boissonneault - # Fix explicit version of aclocal (specified 1.14). Replaced with version 1.15 which corresponds to the 20150215 Autotools 'igraph-%(version)s-fix-aclocal-version.patch' ] -- GitLab From f134c4ca7dcb46bb0eedae01d0fe4c05115e013e Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Thu, 23 Feb 2017 10:06:10 +1030 Subject: [PATCH 310/818] error corrected --- .../easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb | 20 ++++++------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb index 25c303ad85..2075adf0b4 100644 --- a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -3,35 +3,27 @@ # Homepage: https://www.adelaide.edu.au/phoenix/ # # Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Manuel Sepulveda Escobedo +# Authors:: Robert Qiao , Exe Escobedo # License:: # # Notes:: ## +easyblock = 'BinariesTarball' + name = 'meRanTK' version = '1.1.1b' -easyblock = 'BinariesTarball' homepage = 'http://www.icbi.at/index.html' description = """meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.icbi.at/software/meRanTK/downloads'] -sources = ['%s/meRanTK-%s.zip' %(version,version,)] - -dependencies = [ -] +source_urls = ['http://www.icbi.at/software/meRanTK/downloads/%(version)s/'] +sources = ['meRanTK-%(version)s.zip'] sanity_check_paths = { - 'files':['bin/meRanAnnotate'], - 'files':['bin/meRanCall'], - 'files':['bin/meRanCompare'], - 'files':['bin/meRanGs'], - 'files':['bin/meRanGt'], - 'files':['bin/meRanT'], - 'dirs':[], + 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], } moduleclass = 'bio' -- GitLab From 1b573a83426da3b37a07896b9bbdbdc5cdcea9dc Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 23 Feb 2017 14:58:00 +1030 Subject: [PATCH 311/818] Style fixed --- easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb index 2075adf0b4..0d549f7977 100644 --- a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -23,7 +23,8 @@ source_urls = ['http://www.icbi.at/software/meRanTK/downloads/%(version)s/'] sources = ['meRanTK-%(version)s.zip'] sanity_check_paths = { - 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], + 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 637f19f50c5b6cf5e59b6e83d016a7634c60e52e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:14:15 +0100 Subject: [PATCH 312/818] prefer OpenSSL as OS dep in easyconfig for Python 2.7.11 w/ iomkl/2016.07 --- .../easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb index c445811709..ceffc4847a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -23,14 +23,14 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), - ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), ] -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 -- GitLab From 5b23bc5e4ac2d1e0c0fcfef2211f17e4b3e846d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:20:47 +0100 Subject: [PATCH 313/818] comments should start with '# ' --- easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb | 4 ++-- .../a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb | 6 +++--- .../easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb | 2 +- .../c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb | 2 +- .../c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb | 2 +- .../c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb | 2 +- easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb | 2 +- .../CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 -- .../CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 -- .../DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb | 2 +- .../DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb | 2 +- ...-library-20130406-045632_pre-release-3_Linux-x86_64.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb | 2 +- .../g/Ghostscript/Ghostscript-9.20-foss-2016b.eb | 2 +- .../g/Ghostscript/Ghostscript-9.20-intel-2016b.eb | 2 +- .../gencore_variant_detection-1.0.eb | 2 +- .../h/hanythingondemand/hanythingondemand-3.0.0-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.1-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.2-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.3-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.4-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.0-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.1-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.2-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.3-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.4-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.2.0-cli.eb | 8 ++++---- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- .../i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb | 6 +++--- .../i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb | 6 +++--- .../k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 2 +- .../k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 2 +- easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- .../easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb | 2 +- .../easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- .../easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 2 +- .../l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb | 2 -- .../m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 4 ++-- .../m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 4 ++-- .../m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 4 ++-- .../m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 4 ++-- .../m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb | 2 +- .../m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb | 2 +- .../m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb | 2 +- .../m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 ++-- .../p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb | 4 ++-- .../ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb | 2 +- .../ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb | 1 - .../Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 +-- .../p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 5 +++-- .../easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 2 +- .../pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb | 4 ++-- .../p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 4 ++-- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 2 +- 160 files changed, 215 insertions(+), 221 deletions(-) diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index 1e7fda13a1..bfa52a0b28 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -12,8 +12,8 @@ description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """ toolchain = {'name': 'dummy', 'version': 'dummy'} -#You need to create an account to download the source -#from https://www.nitrc.org/frs/?group_id=370 +# You need to create an account to download the source +# from https://www.nitrc.org/frs/?group_id=370 sources = ['ashs_Linux64_%(version)s.tgz'] checksums= ["07fea2883b856af8797b200212b72e71"] diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb index 9a71b607be..5f9521e1fe 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb @@ -11,13 +11,13 @@ source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-forge-%(version)s.tar'] # Example of templates usage -#templates = [ +# templates = [ # 'kebnekaise.qtf', # 'kebnekaise-gpu.qtf', -#] +# ] # Example of sysconfig usage -#sysconfig = 'system.config.hpc2n' +# sysconfig = 'system.config.hpc2n' # license file license_file = HOME + '/licenses/allinea/license.lic' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 361932b89c..9469af37f5 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -30,6 +30,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 02e855be5b..264b5296c0 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -30,6 +30,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 2877853840..f3e4ae2e16 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -30,6 +30,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 58e8cf38d8..3ccec7b3ec 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -31,6 +31,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index da15149173..37790b2b2b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -31,6 +31,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index d2d24de2f8..48fab89b05 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index 3f05bda0e8..3f2240e2f4 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index d7856c8fa2..0bb8d3c531 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index a342fa3e4d..ab7844bff7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 3901df0ef7..9167bcb56a 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index f74362241f..063d865aaf 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb index 29bf068b6a..7309705748 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb index e48888855e..4a280ff234 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb index 63080d8ef9..7f469a05ee 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb index ab9ee385d7..c03250720b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index e6f905f409..b5f1d052ce 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb index 130d3553bd..bbe947dc70 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 5e1447f0f0..e4ebb6e711 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb index 135315981b..c20cd926c3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb index b8e7064fcc..86657cbc54 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb index 86f4ad5681..b454e2d862 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb index 635df8455b..a7b9c8e81a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb index ba3ca2e1aa..4e830d782c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb index 21bbc29383..d1f1daadea 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb index 1a599467bd..48abe1a308 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb @@ -20,7 +20,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb index 5702e9976d..0302fdf415 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb index 87dc8ebec4..d1277a5a59 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb index 638514df1f..e56455fcc7 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index df5823de42..fe1b6c58f6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb index db841bbaef..1b59bc2fe5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb index 0204c038c7..3888217474 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb index 36a239c230..d031a47e1d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index e6beb92bee..1b238fe9f8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb index cfb29da8c6..f96062a9f5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb index f5527c16d6..19d8dce097 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb index 383be7ac07..3b0f2cdbc8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb index 7deb175b91..591130db85 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb index 31b70f1b8a..a1da8e92c6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb index a70441375c..b649d19572 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 619aaa3ab8..d09d0de5fa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb index 9075c094fb..46fe821879 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb index 42e9b3b3bd..1c577d44b5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb index 1f3daa3224..4634580e57 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb index 6d07f31ebd..7df8000a04 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb index b68274e5b4..b3ea9ff87e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb index 97b2282312..0fcaa0288c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb index d5ca429e05..8955a08ffe 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb index c1386c78f8..bdffe9630d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb index 40d915d152..f6bb9a5e3d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb index aa63de70da..476a5bdd98 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb index adb0724437..31ce4be00a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb index b6e496837c..6f2f602755 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb index 5b3221d0bf..bb9e39dab2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb index b364332ea0..e5028321c6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb index e459f784ef..b93ad04bc3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb index 0464c9024d..dec6da7b0d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb index 2c33988a54..f118a4b2fb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb index d34361f252..bf60245a75 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb @@ -40,7 +40,7 @@ parallel = 1 # regression test runtest = False # regression test reports failures -#ignore_regtest_fails = True +# ignore_regtest_fails = True # build type type = 'psmp' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb index e7bf9550c7..20bfca4976 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb @@ -37,7 +37,7 @@ parallel = 1 # regression test runtest = False # regression test reports failures -#ignore_regtest_fails = True +# ignore_regtest_fails = True # build type type = 'psmp' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 50a365b60a..45b63f0380 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -12,8 +12,6 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html ## -#easyblock = 'ConfigureMake' - name = 'CUDA' version = '7.5.18' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index dc4d389baf..72651d5b54 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -12,8 +12,6 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html ## -#easyblock = 'ConfigureMake' - name = 'CUDA' version = '7.5.18' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb index 6491ebe755..81827042d8 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1q'), + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb index 0a65c07d0f..d5862a7c5a 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1q'), + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb index 009df93cd7..b7ffec63fe 100644 --- a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb +++ b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb @@ -26,7 +26,7 @@ source_urls = [('http://sourceforge.net/projects/gemlibrary/files/gem-library/Bi # core_i3 is the recommended version by developers. Better performance sources = ['GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2'] # if core_i3 version doesn't work for you, try core_2 version below -#sources = ['GEM-binaries-Linux-x86_64-core_2-20130406-045632.tbz2'] +# sources = ['GEM-binaries-Linux-x86_64-core_2-20130406-045632.tbz2'] # only Linux_x86-64 binaries are provided so we skip build_step. # We just use the MakeCp block to copy each file to the right destination folder (mainly the man files) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb index 5fbe4acc9a..d00a71f2d8 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb index 6189b95fa0..3994be6bc4 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb index 5440f25394..abea13b1ce 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -27,7 +27,7 @@ dependencies = [ # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index 5e9cfedc47..f2525337c6 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -27,7 +27,7 @@ dependencies = [ # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb index 00035603e7..6b8d559ccc 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb @@ -30,7 +30,7 @@ dependencies = [ # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb index 7305497c37..c65da40120 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('LibTIFF', '4.0.6'), ] -#Do not use local copies of zlib, jpeg, freetype, and png +# Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index d3f76e106a..b89382f6a1 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('LibTIFF', '4.0.6'), ] -#Do not use local copies of zlib, jpeg, freetype, and png +# Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index b799146d37..f4f2214acc 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('Anaconda3', '4.0.0')] # Use one of the following - either an environment.yml file or a remote environment definition -#environment_file = '/path/to/conda-environment.yml' +# environment_file = '/path/to/conda-environment.yml' remote_environment = "nyuad-cgsb/%(name)s_%(version)s" sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb index 3c591a65e9..f18772cba0 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb index c6c633599b..7d698aa331 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb index a6a417a8dc..79d83ae249 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb index 996a654cea..be5a34157b 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb index 754319d620..e614c725c0 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb index 2c68b1bfaa..82c6cbe980 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb index 3f8a48b472..e91b71bb90 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb index cb9ae64332..4862029e81 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb index 4846e39a8e..9e46040159 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb index 275b2940c7..882a63bafc 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb index 7e255dbc21..da0110ba9d 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 88b4f2e32e..52f0e797fd 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -#modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index fccdce2d50..681a2da8cf 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -#modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb index df95bd6282..15948e83d4 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -116,9 +116,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '4.2.0', { + # ('nbconvert', '4.2.0', { # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - #}), + # }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb index d3bbfe47b7..73b84816cd 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -116,9 +116,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '4.2.0', { + # ('nbconvert', '4.2.0', { # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - #}), + # }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index 9a8c7fce6d..bbfde4273f 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -13,7 +13,7 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.""" -#Part is compiled with CXX, the rest is in Perl +# Part is compiled with CXX, the rest is in Perl toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb index fc353606af..a1be8e5709 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -13,7 +13,7 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.""" -#Part is compiled with CXX, the rest is in Perl +# Part is compiled with CXX, the rest is in Perl toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb index 128c5bbc07..27a91f92c0 100644 --- a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb +++ b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb @@ -12,7 +12,7 @@ description = """Visually Informed LeadOpt""" toolchain = {'name': 'dummy', 'version': 'dummy'} -#You need to get the software manually from http://www.biosolveit.de/LeadIT/index.html +# You need to get the software manually from http://www.biosolveit.de/LeadIT/index.html sources = ['leadit-%(version)s-Linux-x64.tar.gz'] checksums = ['363fa557861c4d109fd595ab895df3fd'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb index bd766f2e39..aaf083cf04 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' patches = ['libxc-%(version)s-fix-initialization.patch'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb index f86e8ff9fb..0d7ebaf5fb 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' patches = ['libxc-%(version)s-fix-initialization.patch'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 4c45b545b5..635c9b4d96 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb index 8276d5a07e..dc228fe31b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb index 0bf711caf0..f440f02af5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index e6561d3ed6..df5b0a2ac4 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb index c631b87e66..674453ff55 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 3bee3b3d9c..2ce787f05e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb index d9d2ff8c6b..d3176a0e56 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb index 254367cee7..f3870dc3fb 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 13f7f941b6..80de4c9f97 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb index ae74d150b0..7a2ba48de6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -21,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.so'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb index b029d7950c..8e7a6d0b88 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index 7590c8664b..42d53d0949 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 96aab1d178..2d6dda37b8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 969028930d..8733225f52 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 4f8d72a634..40280eac70 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index a8378f3087..ef6bdb3052 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index fd83352b30..b63d48a898 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 951b7f0605..67f7a66326 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb index 6921c06b50..58524fdeb0 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb @@ -23,8 +23,6 @@ dependencies = [ ('libpthread-stubs', '0.3'), ] -#preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " - sanity_check_paths = { 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', '-randr', '-record', '-render', '-res', '-screensaver', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 3f895315b2..93b02acda8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -50,14 +50,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --disable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl""" # package-config files for os dependencies are in an os specific place -#preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 592c4a1182..3ebe66dd51 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -47,14 +47,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 2bd0ff0f94..2631598232 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -46,14 +46,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index a22cf02d69..244c4f1427 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -46,14 +46,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index 231d3ed99e..81337fce92 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 7b54c5a0b7..84db881b8b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index ecd0aaeeb3..9a2892bda4 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index 18bebf34fd..8fe85b43fb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index 09f90b3879..c0ae4f1fc2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb index c80d4d1ee1..51f747c203 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb index 251958da52..678309eb8a 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb index 22912ecf4a..b2738fff57 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb index 47852f7b9a..3639fc72f4 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index 3a54e8b3b2..8e7a8e3488 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index 870b4ca0ec..1aae2d7107 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb index 1291a991d1..1474c30ba6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb index fe4211f53c..e83941b54c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb index 23704a985e..9be631f2d3 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index b11768a150..d1b44dfae9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb index 32dd146e23..1c0d99523c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index abbe566e01..28a8a8d5c5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index 9dd493110f..92f08781e2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index 3879abb7bd..0b62a315f7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index 21a2a7c815..85f10c536a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index ba23eaadbf..143c9edae7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -44,7 +44,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index bd9785f7cc..1e915a802f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index 16af9a1249..30835b6878 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index c183debe56..b1e3b0dad6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index ba2f665b5b..19c2176d82 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index dbc806f461..d346fc16be 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index d0e54d0995..4cb827eecc 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 5b1245248a..fb9d354480 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -42,7 +42,7 @@ dependencies = [ ('GST-plugins-base', '1.6.4'), ] -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index bd5181fa1c..52aa30e629 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -43,7 +43,7 @@ dependencies = [ ] preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index e7f6df5043..fc8dc13e40 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -44,7 +44,7 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb index ed0569f101..249aec45bf 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -35,10 +35,10 @@ builddependencies = [ configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' # CMake will pick mpiexec by default and this fails with intel MPI -#configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' +# configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' # The tests don't work with MPI (most of them hang or fail) -# ref: https://github.com/psi4/psi4/pull/436#issuecomment-230519769 +# ref: https://github.com/psi4/psi4/pull/436# issuecomment-230519769 runtest = False moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb index c8116fe14f..4a341a8548 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb @@ -39,7 +39,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +# configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb index 2e184fd801..c862a27b0b 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb @@ -38,7 +38,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +# configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index 974e57d87c..d205929d06 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -21,7 +21,6 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index ed40bed006..4127452393 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -21,14 +21,13 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index dcac389893..571dd12dc1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -29,7 +29,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # We hide this by default since users should not use it in production, high-performance Python should be delivered at # compiler level with a default extension set -#hidden = True +# hidden = True # bare installation: only known module deps for GCCcore tools included exts_list = [] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb index c83dff187b..6f474dc2c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb @@ -19,8 +19,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - #nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 7bdd55756a..b91c6a4a7d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -21,8 +21,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index f49b2ff085..3034157afb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -24,7 +24,7 @@ dependencies = [ ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2h'), + # ('OpenSSL', '1.0.2h'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb index 908370bc3a..098af10b8c 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb @@ -18,8 +18,8 @@ sources = ['%s.tar.gz' % commit_id] patches = ['%(name)s-%(version)s_openblas.patch'] -#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus -#Check scripts/buildThirdParty.sh +# pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +# Check scripts/buildThirdParty.sh builddependencies = [ ('CMake', '3.4.3'), ('CastXML', '20160617'), diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index 3b3bd56fa2..8ab67d6ce0 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -18,8 +18,8 @@ sources = ['%s.tar.gz' % commit_id] patches = ['%(name)s-%(version)s_openblas.patch'] -#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus -#Check scripts/buildThirdParty.sh +# pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +# Check scripts/buildThirdParty.sh builddependencies = [ ('CMake', '3.4.3'), ('CastXML', '20160617'), diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 499d383ce4..ab47b2f132 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -54,7 +54,7 @@ exts_list = [ 'utils', # non-standard libraries, should be specified with fixed versions! # Rmpi segfaults (on some systems) when built with goolf/1.7.20? - #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + # ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-5', ext_options), diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index cc50539ec7..f0e1274759 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), ('PCRE', '8.12'), ('CFITSIO', '3.34'), - #('graphviz', '2.34.0'), Graphviz is optional, not in EB yet. + # ('graphviz', '2.34.0'), Graphviz is optional, not in EB yet. (python, pyver), ] -- GitLab From 65ef33d28f518a9d63262dc73483420b111e3e31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:46:11 +0100 Subject: [PATCH 314/818] fix long lines and space issues --- .../easyconfigs/a/ASHS/ASHS-rev103_20140612.eb | 10 +++++----- .../a/ant/ant-1.10.0-Java-1.8.0_112.eb | 5 +++-- .../a/ant/ant-1.9.7-Java-1.8.0_92.eb | 5 +++-- .../b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 3 ++- .../b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb | 1 - .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- .../c/ctffind/ctffind-4.0.17-intel-2015b.eb | 3 ++- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 17 +++++------------ ...ator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb | 5 +++-- .../g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb | 2 +- .../Ghostscript/Ghostscript-9.20-foss-2016b.eb | 4 +++- .../Ghostscript/Ghostscript-9.20-intel-2016b.eb | 4 +++- easybuild/easyconfigs/g/gompi/gompi-2016.09.eb | 4 ++-- .../i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb | 2 +- .../i/intelcuda/intelcuda-2016.10.eb | 3 ++- ...Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 2 +- ...Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 2 +- .../l/libxc/libxc-2.2.3-foss-2016b.eb | 2 +- .../l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- .../l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- .../l/libxc/libxc-3.0.0-intel-2016a.eb | 2 +- .../l/libxc/libxc-3.0.0-intel-2016b.eb | 2 +- .../Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 5 +++-- .../Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 5 +++-- .../Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 5 +++-- .../o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 ++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 ++-- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb | 12 ++++++------ .../PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 12 ++++++------ .../PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb | 2 +- .../p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 3 ++- .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 3 ++- .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 3 ++- .../Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb | 3 ++- .../Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 3 ++- .../p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 3 ++- .../p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 3 ++- .../p/Python/Python-2.7.11-goolf-1.7.20.eb | 5 +++-- ...ython-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 7 ++++--- .../Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 8 +++++--- .../p/Python/Python-2.7.3-foss-2015b.eb | 3 ++- .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-2.7.3-goolf-1.5.14.eb | 3 ++- .../p/Python/Python-2.7.3-ictce-5.2.0.eb | 3 ++- .../p/Python/Python-2.7.3-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-2.7.3-intel-2015a.eb | 3 ++- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 3 ++- .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 3 ++- .../p/Python/Python-2.7.8-foss-2014b.eb | 3 ++- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 3 ++- .../p/Python/Python-2.7.8-ictce-7.1.2.eb | 3 ++- .../p/Python/Python-2.7.8-intel-2014.06.eb | 3 ++- .../p/Python/Python-2.7.8-intel-2014b.eb | 3 ++- .../p/Python/Python-2.7.8-intel-2015a.eb | 3 ++- .../Python/Python-2.7.9-CrayGNU-2015.06-bare.eb | 3 ++- .../p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 8 +++++--- .../Python/Python-2.7.9-CrayGNU-2015.11-bare.eb | 3 ++- .../p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 8 +++++--- .../p/Python/Python-2.7.9-GCC-4.8.4-bare.eb | 3 ++- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015.05.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015a.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015b.eb | 3 ++- .../p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 3 ++- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 3 ++- .../p/Python/Python-2.7.9-goolf-1.5.16.eb | 3 ++- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 3 ++- .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 3 ++- .../p/Python/Python-2.7.9-intel-2015a.eb | 3 ++- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-3.3.2-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-3.3.2-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-3.4.1-intel-2014b.eb | 3 ++- .../p/Python/Python-3.4.1-intel-2015a.eb | 3 ++- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 ++- .../p/Python/Python-3.5.0-intel-2015b.eb | 3 ++- .../p/Python/Python-3.5.1-foss-2015a.eb | 3 ++- .../p/Python/Python-3.5.1-foss-2016a.eb | 3 ++- .../p/Python/Python-3.5.1-intel-2016a.eb | 3 ++- ...pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb | 2 +- .../QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 11 +++++------ 88 files changed, 198 insertions(+), 137 deletions(-) diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index bfa52a0b28..a251f6e6b4 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Tarball" +easyblock = 'Tarball' name = 'ASHS' version = 'rev103_20140612' @@ -16,14 +16,14 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # from https://www.nitrc.org/frs/?group_id=370 sources = ['ashs_Linux64_%(version)s.tgz'] -checksums= ["07fea2883b856af8797b200212b72e71"] +checksums = ['07fea2883b856af8797b200212b72e71'] modextravars = {'ASHS_ROOT': '%(installdir)s'} sanity_check_paths = { - 'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", - "bin/ashs_util_makepdf.sh"], - 'dirs': ["ext"] + 'files': ['bin/ashs_main.sh', 'bin/ashs_template_qsub.sh', 'bin/ashs_train.sh', + 'bin/ashs_util_makepdf.sh'], + 'dirs': ['ext'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb index 2d88d28b75..d2ebd37189 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -3,8 +3,9 @@ version = '1.10.0' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb index 175bb2628a..4c6e292088 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb @@ -3,8 +3,9 @@ version = '1.9.7' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb index 25b2cd8bb7..a0b996743d 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -9,7 +9,8 @@ name = 'BayeScEnv' version = '1.1' homepage = 'https://github.com/devillemereuil/bayescenv' -description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.""" +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables + to detect local adaptation.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb index de8bcce297..2902acfde6 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -12,7 +12,6 @@ homepage = 'http://cmpg.unibe.ch/software/BayeScan/' description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" -# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 3abe5c93c9..4000cc8571 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', 'extract_reads', 'filter_reads', 'index_and_search']], - 'dirs' : ['doc', 'include'] + 'dirs': ['doc', 'include'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index 8c2ecba76b..60152e7602 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -22,7 +22,8 @@ dependencies = [('GSL', '1.16')] # when running ./configure in the root folder it fails. # application doesn't provide a 'make install' prebuildopts = 'mkdir build && cd build && ' -prebuildopts += ' ../configure --enable-static --disable-debug --enable-optimisations --enable-openmp FC=${FC} F77=${F77} && ' +prebuildopts += " ../configure --enable-static --disable-debug --enable-optimisations --enable-openmp " +prebuildopts += "FC=${FC} F77=${F77} && " files_to_copy = [(['build/ctffind'], 'bin'), 'doc', 'scripts'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 4851fc5541..75d318f670 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -46,18 +46,11 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': [ - 'lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, - 'lib/libelpa_openmp.a', 'lib/libelpa_openmp.%s' % SHLIB_EXT, - 'lib/libelpatest.a', 'lib/libelpatest.%s' % SHLIB_EXT, - 'lib/libelpatest_openmp.a', 'lib/libelpatest_openmp.%s' % SHLIB_EXT, - 'share/doc/elpa/examples/config.h', - 'share/doc/elpa/examples/config-f90.h', - ], - 'dirs': [ - 'bin', 'include/elpa-%(version)s/elpa', - 'include/elpa-%(version)s/modules', 'lib/pkgconfig', - ], + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT, 'lib/libelpatest.a', 'lib/libelpatest.%s' % SHLIB_EXT, + 'lib/libelpatest_openmp.a', 'lib/libelpatest_openmp.%s' % SHLIB_EXT, 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h'], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb index f9d3b4a7b5..5e8c01ab2d 100644 --- a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb +++ b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb @@ -31,8 +31,9 @@ sources = [ dependencies = [ ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] # openssl required by libStatgen diff --git a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb index f302d9f398..238da5f765 100644 --- a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb @@ -22,7 +22,7 @@ configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' runtest = 'check' sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['gp2c', 'gp2c-run',]], + 'files': ['bin/%s' % binfile for binfile in ['gp2c', 'gp2c-run']], 'dirs': ['bin'] } diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb index c65da40120..d7b08e9fef 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -10,7 +10,9 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] sources = ['ghostscript-%(version)s.tar.gz'] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index b89382f6a1..eed125d9f6 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -10,7 +10,9 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] sources = ['ghostscript-%(version)s.tar.gz'] dependencies = [ diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb index d4b83fb9a0..7e7b36e603 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -13,8 +13,8 @@ gccver = '6.2.0-2.27' # compiler toolchain dependencies dependencies = [ - ('GCC', gccver), # includes both GCC and binutils - ('OpenMPI', '2.0.1', '', ('GCC', gccver)), + ('GCC', gccver), # includes both GCC and binutils + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb index 1c64db33bd..66d029ece5 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb @@ -13,7 +13,7 @@ homepage = 'https://github.com/chaos/ior' description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. """ -toolchain = {'name': 'foss', 'version': '2016a' } +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [('https://github.com/chaos/ior/archive/')] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index 82121910a8..14c19568ad 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -4,7 +4,8 @@ name = 'intelcuda' version = '2016.10' homepage = '(none)' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, + Intel MPI & Intel MKL, with CUDA toolkit""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index bbfde4273f..02cc25cfec 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix ='-Perl-%(perlver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb index a1be8e5709..af61c387aa 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix ='-Perl-%(perlver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 8733225f52..2ef9de2a2d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 40280eac70..80e9889a84 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index ef6bdb3052..bd3cb81b7c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index b63d48a898..9417deb550 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 67f7a66326..a251dac24c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 93b02acda8..41d6a64d37 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -54,7 +54,7 @@ dependencies = [ # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --disable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl""" +configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place # preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 3ebe66dd51..8b03ae9140 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -50,8 +50,9 @@ dependencies = [ # osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place # preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 2631598232..5224023e11 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -49,8 +49,9 @@ dependencies = [ # osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place # preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 244c4f1427..ec21cce29c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -49,8 +49,9 @@ dependencies = [ # osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place # preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index fb9d354480..141e1f7cdd 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -67,8 +67,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 52aa30e629..23de8de267 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -68,8 +68,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index fc8dc13e40..0b6f2141a7 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -69,8 +69,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index c76887ac30..261f83dd09 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -32,16 +32,16 @@ exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ ('ExtUtils::Depends', '0.405', { - 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('ExtUtils::PkgConfig', '1.15', { - 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('Getopt::Long', '2.48', { - 'source_tmpl': 'Getopt-Long-2.48.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], }), ('Pod::Usage', '1.68', { 'source_tmpl': 'Pod-Usage-1.68.tar.gz', diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index 4dc47a8df2..f2db549906 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -30,16 +30,16 @@ exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ ('ExtUtils::Depends', '0.405', { - 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('ExtUtils::PkgConfig', '1.15', { - 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('Getopt::Long', '2.48', { - 'source_tmpl': 'Getopt-Long-2.48.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], }), ('Pod::Usage', '1.68', { 'source_tmpl': 'Pod-Usage-1.68.tar.gz', diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb index 249aec45bf..57e1bb653a 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.5.2'), -# ('Perl', '5.22.1', '-bare'), # for the test suite + # ('Perl', '5.22.1', '-bare'), # for the test suite ] configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index e815cc69b5..ace4711442 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -3,7 +3,8 @@ version = '2.5.6' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 809068de30..b1bdb4f782 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -3,7 +3,8 @@ version = '2.5.6' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index c781bfe8b7..cc84b14111 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -3,7 +3,8 @@ version = '2.5.6' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb index fd80fddc40..edaa0f4fa5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb @@ -3,7 +3,8 @@ version = '2.7.10' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index 6e9aa1f7c4..ac622805c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -3,7 +3,8 @@ version = '2.7.10' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index d69b594b08..4289f275f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -5,7 +5,8 @@ name = 'Python' version = "2.7.11" homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index ab13993dcf..f16c276300 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -5,7 +5,8 @@ name = 'Python' version = "2.7.11" homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index d205929d06..500c945db9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index 4127452393..42a08985d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -23,11 +23,12 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), - ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), ] -# osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index 571dd12dc1..01b2892c87 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -3,7 +3,8 @@ version = '2.7.12' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} toolchainopts = {'pic': True} @@ -21,8 +22,9 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.14.1'), - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index c93dab2804..bb77d83c1d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 53cdae92ab..0cda45ec7d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 4cd83e24d0..4ef1bfeaeb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 2608210a17..12a347ef6d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 4ffdd56f78..6265b2329d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 35bbb97553..a22416f124 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index d2f51e3f22..d9a96be894 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.5' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index c0ac0d38b1..48e0894d30 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.5' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 513384d5b5..e6e366e13c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.5' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 95ff34f3f9..384ccabeee 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.6' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 055543dc24..91008ef87d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.6' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 0409f54975..9f687fe594 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 2a90fee410..5f8e6aeeb0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index d975d85c2d..95e0f82630 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index dca27371ed..18384a6b3c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2014.06'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index a7d56bba16..dc5adffe37 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 6b2fccea28..c914576c6c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb index 92748077e8..ceb75f485b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True, 'opt': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index a0d5fb01e5..c42116cc9a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} @@ -19,8 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb index f7679002a1..46d5881734 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True, 'opt': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index eb90e5f158..e020765a41 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} @@ -19,8 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb index 6f474dc2c1..7040f073ac 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index a2e4addace..bfaa856129 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 5ca1dda84e..6bb38e7647 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'https://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index e9063410df..a0543f97f8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index b636f6b2ef..04c7ab534f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 82282d02d9..47705d9de9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index c78274679f..e7e8e929a0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'gompi', 'version': '1.5.16'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 987f0852f6..568e58c6d4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index 37abf12093..3e3d722c5f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index b91c6a4a7d..39c33c3855 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'https://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index c672a429fd..0a241766ab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 24081c5cf8..bb506a20b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index fc5033662d..e164d75eb8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.2.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 1fe945390a..7fc679ddfb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.2.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 0dc65b97ca..5b5ea68742 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.3.2' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index 97e6c04ce7..8ba5022eb1 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.3.2' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index ba9c2f40b2..948d875463 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.4.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 910cb21e5c..db1c3e7576 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.4.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 8f08cf73e4..3ff51e790b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.4.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 825c8e6b10..f46cf60244 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.0' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 68a366030d..a4f85640e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index edc992932d..8d085679d5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 395e40515b..8187598200 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb index 098af10b8c..3e9cb1c1a3 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb @@ -58,7 +58,7 @@ installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', - 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']] + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 09b026a284..f15e4b6ae5 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -21,11 +21,11 @@ sources = [ 'neb-%(version)s.tar.gz', 'PHonon-%(version)s.tar.gz', 'pwcond-%(version)s.tar.gz', - 'xspectra-%(version)s.tar.gz' , - 'PWgui-%(version)s.tar.gz' , - 'EPW-%(version)s.tar.gz' , - 'test-suite-%(version)s.tar.gz' , - 'GWW-%(version)s.tar.gz' , + 'xspectra-%(version)s.tar.gz', + 'PWgui-%(version)s.tar.gz', + 'EPW-%(version)s.tar.gz', + 'test-suite-%(version)s.tar.gz', + 'GWW-%(version)s.tar.gz', ] source_urls = [ 'http://files.qe-forge.org/index.php?file=', # Almost all @@ -55,4 +55,3 @@ buildopts = 'all tddfpt neb xspectra ph ' parallel = 1 moduleclass = 'chem' - -- GitLab From 09eafdcf59c57495cab20f9adf6d8205bc256d6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:52:52 +0100 Subject: [PATCH 315/818] fix more minor style issues in Python easyconfigs --- .../p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb | 5 +++-- .../p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 5 +++-- .../p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb | 5 +++-- .../p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 7 ++++--- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 7 ++++--- 20 files changed, 62 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb index edaa0f4fa5..492d137f68 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index ac622805c5..02428a8c5e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index c914576c6c..a19c3193df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] # order is important! diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb index ceb75f485b..b60dac8832 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb @@ -18,8 +18,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb index 46d5881734..8249b3b9b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb @@ -18,8 +18,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index bfaa856129..4492ecb9d7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 6bb38e7647..0e5c8bdaf5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index a0543f97f8..ed68c4c304 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 04c7ab534f..50b5d85a22 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 47705d9de9..954cb1d6c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index e7e8e929a0..1ef84a7f5f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -19,8 +19,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 568e58c6d4..2117038315 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index 3e3d722c5f..de0245d75a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index 0a241766ab..ca9022ba60 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index bb506a20b0..dfd615f248 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 3ff51e790b..fa4d5db712 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -20,8 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index f46cf60244..7f32b2fbd5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index a4f85640e5..34b680443b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -24,8 +24,9 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 8d085679d5..f17ad6e258 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -24,8 +24,9 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev')] @@ -99,7 +100,7 @@ exts_list = [ }), ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + }), ('pyparsing', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 8187598200..bba87219ba 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -24,8 +24,9 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev')] @@ -103,7 +104,7 @@ exts_list = [ }), ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + }), ('pyparsing', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), -- GitLab From a87550736263fa0a6f625be0b4dae3f18f9c018c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:03:18 +0100 Subject: [PATCH 316/818] add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep --- .../y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb index 5f79b0294c..e82ea4a1ae 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb @@ -32,6 +32,7 @@ dependencies = [ ('SQLite', '3.13.0'), ('VTK', '7.1.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [ @@ -58,4 +59,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' -- GitLab From e1923aef1159c638469a084388ff46a67801f6ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:06:43 +0100 Subject: [PATCH 317/818] add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep --- .../easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 3 +++ .../y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb | 3 +++ .../y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 3 +++ .../y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index a6e0dada54..eeebc684bc 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -34,6 +34,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [('CMake', '3.5.2')] @@ -57,4 +58,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb index 4d7005749a..4610fe64fd 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb @@ -34,6 +34,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [('CMake', '3.5.2')] @@ -57,4 +58,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index 541a3b67c8..64230623c1 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -34,6 +34,7 @@ dependencies = [ ('SQLite', '3.13.0'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [ @@ -60,4 +61,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb index 1c86ea984c..5623f2e81c 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb @@ -33,6 +33,7 @@ dependencies = [ ('SQLite', '3.13.0'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [ @@ -59,4 +60,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' -- GitLab From 00c1bb2312d09860ab51e112128e7193bc8a4c38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:33:55 +0100 Subject: [PATCH 318/818] add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library --- .../Boost-1.61.0-intel-2016a-Python-2.7.11.eb | 2 ++ .../b/Boost/Boost-1.61.0-intel-2016a.eb | 2 ++ .../Boost-1.61.0-intel-2016b-Python-2.7.12.eb | 2 ++ .../b/Boost/Boost-1.61.0-intel-2016b.eb | 2 ++ .../b/Boost/Boost-1.61_fix-make_array-icpc.patch | 14 ++++++++++++++ .../Boost-1.62.0-intel-2016b-Python-2.7.12.eb | 2 ++ .../Boost-1.63.0-intel-2016b-Python-2.7.12.eb | 2 ++ 7 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb index 822d74b107..0ac767fef8 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb index 7840698ed4..526e2b54e1 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb index 015aad2716..918d0a5af6 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb index 67f6199614..d76c8ae2bc 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch b/easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch new file mode 100644 index 0000000000..f7ffa6aa0d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch @@ -0,0 +1,14 @@ +fix bug with make_array/array_wrapper introduced in Boost v1.61; cfr.: +* https://svn.boost.org/trac/boost/ticket/12516 +* https://github.com/boostorg/serialization/pull/46 (source of this patch) +--- boost_1_63_0/boost/serialization/array.hpp.orig 2017-02-23 10:38:00.487842679 +0100 ++++ boost_1_63_0/boost/serialization/array.hpp 2017-02-23 10:38:13.918969000 +0100 +@@ -44,7 +44,7 @@ + // note: I would like to make the copy constructor private but this breaks + // make_array. So I try to make make_array a friend - but that doesn't + // build. Need a C++ guru to explain this! +- template ++ template + friend const boost::serialization::array_wrapper make_array( T* t, S s); + + array_wrapper(const array_wrapper & rhs) : diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb index 8f21675328..f0e124ea49 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb index b110a50dba..faed7a8d9c 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,8 @@ toolchainopts = {'usempi': True, 'pic': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), -- GitLab From 71e87c695ad1339b3080fed65744883cd89a37c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:57:19 +0100 Subject: [PATCH 319/818] trim spaces --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 52f0e797fd..56a8573d69 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = {'IMINTASSERDB': '/path/to/databases/I-TASSER/%(version)s'} moduleclass = 'bio' -- GitLab From 5e3d994a87ba141c104fef69e57673d596fd18fb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 23 Feb 2017 17:19:38 +0100 Subject: [PATCH 320/818] Set CMAKE_PREFIX_PATH to ncurses install directory Include ccmake in sanity check --- easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb | 4 ++-- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb | 4 ++-- .../c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb | 4 +++- easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb | 4 ++-- 28 files changed, 57 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb index 1a599467bd..3b95ac0d58 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [('binutils', '2.25')] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -26,7 +26,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb index 87dc8ebec4..81d2e3eac3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index df5823de42..7b3c226f7d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake, 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb index db841bbaef..4e67d84e5a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb index 0204c038c7..fe4cdb5cff 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.07'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb index 36a239c230..5737de5e86 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index e6beb92bee..6714702dbc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb index cfb29da8c6..a7d7d549c8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb index 31b70f1b8a..de56aab05c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb index f9e868c77a..38d4964aee 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb @@ -13,10 +13,12 @@ toolchain = {'name': 'CrayGNU', 'version': '2016.03'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '6.0')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb index a70441375c..fe0671660a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 619aaa3ab8..1477d6c586 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb index 9075c094fb..3c398a1b9c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb index 42e9b3b3bd..d9e89130f0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb index 6d07f31ebd..be6f338d1f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb index b68274e5b4..24f53c01f5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb index 97b2282312..d495dc07af 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb index d5ca429e05..26041d2bbc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.25'), @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb index c1386c78f8..520b0309fd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb index 40d915d152..fff0b921eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s-use-gnu11.patch'] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -26,7 +26,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb index aa63de70da..1933c5b5eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.26'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb index adb0724437..4bce1497a6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb index b6e496837c..48141f4592 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb index 5b3221d0bf..f932156e58 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.26'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb index b364332ea0..6c1810956d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.2.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb index e459f784ef..db38350c22 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb index 0464c9024d..7b760d0e31 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb index 2c33988a54..1dc781b04a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 1f87bce8231854d3f77defafd5c9b76e51af0cc6 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 23 Feb 2017 16:32:27 +0000 Subject: [PATCH 321/818] Added an easyconfig with PETSc 3.7.5 and download options rather than relying on existing modules. --- .../PETSc/PETSc-3.7.5-intel-2016a-download.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb new file mode 100644 index 0000000000..a59522d52f --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb @@ -0,0 +1,41 @@ +name = 'PETSc' +version = '3.7.5' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +shared_libs = 1 +pic = 1 + +downloadinstall = True + +dependencies = [('HDF5','1.8.18')] + +configopts = "" +# compiles PETSc shared +configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +# external packages that are downloaded +external_packages = ['mumps', 'ptscotch', 'superlu', 'superlu_dist', 'parmetis', 'metis', 'ml', 'suitesparse', 'hypre', 'prometheus'] +# compiles the external dependencies non-shared +external_packages_shared = "no" +for p in external_packages: + configopts += "--download-%s=yes --download-%s-shared=%s " % (p,p,external_packages_shared) +configopts += "--download-triangle=yes" # download-triangle-shared is not supported + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'numlib' + +modluafooter = """ +family("petsc") +""" + -- GitLab From 1eef7612f698db9570682e01fa845c88a92ec513 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 23 Feb 2017 19:04:49 +0100 Subject: [PATCH 322/818] Fix typo --- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index 7b3c226f7d..85d36d3bbd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake, 'cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 154ccb596730abc6c47f479ce150f1721e6d4dfb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 20:37:54 +0100 Subject: [PATCH 323/818] remove duplicate bzip2 in Yade easyconfig --- .../easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index 64230623c1..bfb9412cfc 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -18,7 +18,6 @@ patches = ['Yade-%(version)s_include-signal.patch'] dependencies = [ ('Boost', '1.61.0', versionsuffix), - ('bzip2', '1.0.6'), ('CGAL', '4.8.1', versionsuffix), ('GDB', '7.11.1', versionsuffix), ('GL2PS', '1.3.9'), -- GitLab From 533f365f73661c4fcf0f53d56118556f94b316e3 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 24 Feb 2017 04:32:04 +0100 Subject: [PATCH 324/818] Switch to lowopt=True for libxc-2.2.* with intel compilers I've noticed that some functionals in LibXC give significantly different results with too much compiler optimization. For example, the energy of a water molecule computed with the TPSS functional changes by 6.5 kJ/mol with lowopt=False. (The problem is in the TPSS correlation functional, somewhere in mgga_c_pkzb.c. I've ruled out numerical integration issues. Similar relative errors appear on every grid point of the tpss_c energy density.) I can only test with libx-2.2.* and intel compilers at the moment. I'll make similar changes for other versions and compilers when the opportunity arises. --- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 1 + 6 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 2ce787f05e..0617eecddd 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 80de4c9f97..954c4b2503 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index 42d53d0949..c266e8d3fa 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 2d6dda37b8..9d234313e3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 80e9889a84..e4360c8222 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index bd3cb81b7c..c15059fd00 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] -- GitLab From 0d488e49be4e453e794e5c4636dc9739f884b874 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 09:26:59 +0100 Subject: [PATCH 325/818] remove custom sanity_check_paths, since it's identical to that used by the R easyblock --- .../easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb | 10 ---------- .../easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb | 10 ---------- .../easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb | 10 ---------- 14 files changed, 140 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb index b12bc8e75d..fddd66f795 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb index 561a883aa5..41c4f5301f 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb index d58882331f..69f1781b69 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb index 8ba729ce15..69437c1b5a 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb index e96756b81d..99f0a85afd 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb index 86f63c2452..b6f9488dc0 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb index a7f037b0a7..6da04393a8 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb index c79a8bd4e8..25ba222aa6 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb index 3c069b9b81..8abe6d999a 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb index 8d427ebb5d..d3eaca313f 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb @@ -23,14 +23,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb index b2aa058997..f34e0f18e6 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb index ee87a80c86..1572f6e35f 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb index 31222cc1f7..b0d2830c75 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb @@ -26,14 +26,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb index 866b40ba81..a2eabbbdcd 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb @@ -23,16 +23,6 @@ dependencies = [ ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - exts_list = [ # default libraries, only here to sanity check their presence 'base', -- GitLab From 4f3fba3ae7d8c413468784e10b38767e18553240 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 24 Feb 2017 11:40:55 +0100 Subject: [PATCH 326/818] Apply CMAKE_PREFIX_PATH/ncurses and ccmake tweak to CMake 3.4.0 and up --- easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb | 4 +++- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb | 4 +++- easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb | 4 +++- 11 files changed, 25 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb index 21bbc29383..53143ba0a0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb index cb117db322..8b223712cc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb @@ -12,10 +12,12 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb index 4f9c1dcfa2..f268f237cd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -21,7 +21,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb index 5702e9976d..0faaa6fe56 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb index 638514df1f..1b0e29c51f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb index f5527c16d6..db51b497b9 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb index 383be7ac07..4095a8cf13 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb index 7deb175b91..9ae7cc86bf 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '7.3.5'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb index c7cd4a579a..9ffba8c3eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb @@ -13,10 +13,12 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb index 1f3daa3224..535e3995e0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb index 412e055df6..701830e871 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -12,10 +12,12 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '6.0')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 05485fb12247fce13d584bb7c41aaa7ff8e325ba Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 24 Feb 2017 14:34:17 +0100 Subject: [PATCH 327/818] Add comment to EBs to explain low optimization settings --- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 0617eecddd..f971a65f6f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 954c4b2503..6cdc9b59df 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index c266e8d3fa..c926977f8e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 9d234313e3..9eb91c2953 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index e4360c8222..203ac28517 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index c15059fd00..f83e57a0da 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] -- GitLab From 99c191768ac31d851c3a2d75d68c3bad9366d2d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 17:58:17 +0100 Subject: [PATCH 328/818] adding easyconfigs: MEGA-7.0.20-1.eb --- easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb new file mode 100644 index 0000000000..4513c7f7b6 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb @@ -0,0 +1,24 @@ +easyblock = 'Tarball' + +name = 'MEGA' +version = '7.0.20-1' + +homepage = 'http://www.megasoftware.net/' +description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools + for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download requires agreeing with license & filling out a form, see http://www.megasoftware.net/ +sources = ['megacc-%(version)s.x86_64.tar.gz'] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ['megacc', 'megaproto'], + 'dirs': ['Examples'], +} + +moduleclass = 'bio' -- GitLab From 9161535b5ebb7766dbb2be4122a1790bd8c64c03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 18:57:57 +0100 Subject: [PATCH 329/818] adding easyconfigs: PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb --- ...ables-3.2.3.1-intel-2016b-Python-2.7.12.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..904febe2a2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.2.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v.%(version)s.tar.gz'] + +patches = ['pyTables-3.2.2-fix-libs.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.17'), + ('LZO', '2.09'), + ('Blosc', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' -- GitLab From 7e533b72c6d1af1130a16882b38e62ba2bc71ace Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 19:47:32 +0100 Subject: [PATCH 330/818] adding easyconfigs: ea-utils-1.04.807-intel-2016b.eb --- .../ea-utils/ea-utils-1.04.807-intel-2016b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb new file mode 100644 index 0000000000..79eae70f31 --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'ea-utils' +version = '1.04.807' + +homepage = 'http://expressionanalysis.github.io/ea-utils/' +description = """Command-line tools for processing biological sequencing data. +Barcode demultiplexing, adapter trimming, etc. + +Primarily written to support an Illumina based pipeline - +but should work with any FASTQs.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ExpressionAnalysis/ea-utils/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['5972b9f712920603b7527f46c0063a09'] + +start_dir = 'clipper' + +prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " +buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' + +builddependencies = [ + ('Perl', '5.24.0'), +] + +dependencies = [ + ('GSL', '2.3'), +] + +files_to_copy = [([ + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' +)] + + +sanity_check_paths = { + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 71a4609f70236b90dea63d66161409d7b2dd314d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2017 08:47:58 +0100 Subject: [PATCH 331/818] fix version (& homepage) in ea-utils easyconfigs --- ...16a.eb => ea-utils-1.04.807-foss-2016a.eb} | 20 +++++++++---------- ...16b.eb => ea-utils-1.04.807-foss-2016b.eb} | 18 ++++++++--------- 2 files changed, 17 insertions(+), 21 deletions(-) rename easybuild/easyconfigs/e/ea-utils/{ea-utils-27a4809-foss-2016a.eb => ea-utils-1.04.807-foss-2016a.eb} (64%) rename easybuild/easyconfigs/e/ea-utils/{ea-utils-27a4809-foss-2016b.eb => ea-utils-1.04.807-foss-2016b.eb} (66%) diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb similarity index 64% rename from easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb rename to easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb index 7cf3821ef3..498218ede9 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb @@ -1,9 +1,9 @@ easyblock = 'MakeCp' name = 'ea-utils' -version = '27a4809' +version = '1.04.807' -homepage = 'https://code.google.com/p/ea-utils/' +homepage = 'http://expressionanalysis.github.io/ea-utils/' description = """Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. @@ -11,12 +11,12 @@ Primarily written to support an Illumina based pipeline - but should work with any FASTQs.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} -source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] -sources = [SOURCE_TGZ] +source_urls = ['https://github.com/ExpressionAnalysis/ea-utils/archive/'] +sources = ['%(version)s.tar.gz'] -checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] +checksums = ['5972b9f712920603b7527f46c0063a09'] start_dir = 'clipper' @@ -38,11 +38,9 @@ files_to_copy = [([ sanity_check_paths = { - 'files': [ - 'bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', - 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall' - ], + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], 'dirs': [] } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb similarity index 66% rename from easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb rename to easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb index e8447b7c64..5bd575648e 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb @@ -1,9 +1,9 @@ easyblock = 'MakeCp' name = 'ea-utils' -version = '27a4809' +version = '1.04.807' -homepage = 'https://code.google.com/p/ea-utils/' +homepage = 'http://expressionanalysis.github.io/ea-utils/' description = """Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. @@ -11,12 +11,12 @@ Primarily written to support an Illumina based pipeline - but should work with any FASTQs.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} -source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] -sources = [SOURCE_TGZ] +source_urls = ['https://github.com/ExpressionAnalysis/ea-utils/archive/'] +sources = ['%(version)s.tar.gz'] -checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] +checksums = ['5972b9f712920603b7527f46c0063a09'] start_dir = 'clipper' @@ -38,10 +38,8 @@ files_to_copy = [([ sanity_check_paths = { - 'files': [ - 'bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', - 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall' - ], + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], 'dirs': [] } -- GitLab From a9f5681fae6e765adb1851e8b1414e6d5f8aecf0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2017 09:05:26 +0100 Subject: [PATCH 332/818] avoid escape double quotes to make tests happy --- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 8cdb56fbdb..3f9e8e96b8 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -27,10 +27,10 @@ start_dir = 'ORTHOMCLV%(version)s' # fix hardcoded paths postinstallcmds = [ 'sed -i"" "s@/usr/bin/perl@$EBROOTPERL/bin/perl@g" %(installdir)s/orthomcl.pl', - 'sed -i"" "s@\\"/.*blastall\\";@\\"$EBROOTBLAST/bin/blastall\\";@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@\\"/.*formatdb\\";@\\"$EBROOTBLAST/bin/formatdb\\";@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@\\"/.*mcl\\";@\\"$EBROOTMCL/bin/mcl\\";@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@\\"/.*ORTHOMCL.*%(version)s/\\";@\\"\\$ENV{\'PWD\'}/\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*blastall@$EBROOTBLAST/bin/blastall@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*formatdb@$EBROOTBLAST/bin/formatdb@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*\(mcl.;\)@$EBROOTMCL/bin/\\1@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*ORTHOMCL.*%(version)s/@\\$ENV{\'PWD\'}/@g" %(installdir)s/orthomcl_module.pm', ] modextrapaths = { -- GitLab From e040c832a322df495cd07b6ead1e677372f96d66 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 25 Feb 2017 12:53:16 +0100 Subject: [PATCH 333/818] Remove redundant toolchainopts (libxc) --- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index f971a65f6f..8c8a06232c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2014b'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 6cdc9b59df..386fc2d5ba 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2015a'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index c926977f8e..eef2248b2a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2015a'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 9eb91c2953..658c339764 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2015b'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 203ac28517..4cb658a639 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2016a'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index f83e57a0da..41bfb6c123 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2016b'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] -- GitLab From 3be2942c3f45d3c59b3a320d691b89724f22021d Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 25 Feb 2017 12:53:43 +0100 Subject: [PATCH 334/818] Also use lowopt=True for libxc-3.0.0 --- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 2 ++ easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index 9417deb550..e89a3a0020 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index a251dac24c..812bf5438b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] -- GitLab From 9588d0ae3e84fedafce93186a6970e13bacfec07 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 25 Feb 2017 13:52:20 +0100 Subject: [PATCH 335/818] Apply lowopt=True to all libxc versions + fix typo in comment Consistency across all eb files reduces the risk that this problem gets reintroduced. --- easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb | 2 ++ easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 2 +- 20 files changed, 32 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb index aaf083cf04..547b2c04e0 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb index 0d7ebaf5fb..ba87bd535c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 635c9b4d96..e944b72c18 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb index dc228fe31b..b9e8982671 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb index f440f02af5..8bd05d53ad 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index df5b0a2ac4..22e411e0a3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb index 674453ff55..51c0a0a535 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 8c8a06232c..45bb52f70b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb index d3176a0e56..39dc38965a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb index f3870dc3fb..3ce46b5609 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 386fc2d5ba..3958efb9f5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb index 7a2ba48de6..3d0a5a1ed8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -9,7 +9,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb index 8e7a6d0b88..5df850f999 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index eef2248b2a..a3e00b811a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 658c339764..3dc273ca2e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 2ef9de2a2d..37456a8225 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2016b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 4cb658a639..56fa742d7d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index 41bfb6c123..0fb5faa09c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index e89a3a0020..e96102336e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 812bf5438b..df3c9b9484 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] -- GitLab From f73bd7e2decc3596222e59328b8e7738384ab2eb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 27 Feb 2017 16:00:51 +0100 Subject: [PATCH 336/818] ppicv->ippicv --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 7d801b065b..0292e9d416 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -41,7 +41,7 @@ dependencies = [ ] #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -ppicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -- GitLab From 5ff58b2b990847489c0d7a8d41b7ff2d22680053 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Feb 2017 20:34:03 +0100 Subject: [PATCH 337/818] add patch required to make building ea-utils with Intel compilers work --- .../ea-utils/ea-utils-1.04.807-intel-2016b.eb | 4 ++- .../ea-utils-1.04.807_include-unistd.patch | 35 +++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb index 79eae70f31..a1c32a3e34 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb @@ -18,10 +18,12 @@ sources = ['%(version)s.tar.gz'] checksums = ['5972b9f712920603b7527f46c0063a09'] +patches = ['ea-utils-%(version)s_include-unistd.patch'] + start_dir = 'clipper' prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " -buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' +buildopts = 'CC="$CC" fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' builddependencies = [ ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch new file mode 100644 index 0000000000..3fb5b110e0 --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch @@ -0,0 +1,35 @@ +fix for 'identifier "unlink" is undefined' and other similar errors + +author: Kenneth Hoste (HPC-UGent) +--- clipper/sparsehash-2.0.2/src/sparsetable_unittest.cc.orig 2017-02-27 19:11:30.059750601 +0100 ++++ clipper/sparsehash-2.0.2/src/sparsetable_unittest.cc 2017-02-27 19:13:28.438628098 +0100 +@@ -32,7 +32,7 @@ + // Since sparsetable is templatized, it's important that we test every + // function in every class in this file -- not just to see if it + // works, but even if it compiles. +- ++#include + #include + #include + #include +--- clipper/sparsehash-2.0.2/src/hashtable_test.cc.orig 2017-02-27 19:49:55.087723317 +0100 ++++ clipper/sparsehash-2.0.2/src/hashtable_test.cc 2017-02-27 19:50:14.027542195 +0100 +@@ -43,7 +43,7 @@ + // Note that since all these classes are templatized, it's important + // to call every public method on the class: not just to make sure + // they work, but to make sure they even compile. +- ++#include + #include + #include + #include +--- clipper/sparsehash-2.0.2/src/time_hash_map.cc.orig 2017-02-27 20:00:27.821672176 +0100 ++++ clipper/sparsehash-2.0.2/src/time_hash_map.cc 2017-02-27 20:00:57.411387012 +0100 +@@ -54,6 +54,7 @@ + // + // See PERFORMANCE for the output of one example run. + ++#include + #include + #include + #ifdef HAVE_INTTYPES_H -- GitLab From 6ac0bc393ce7afcbd1ea2270c0b8c105f885696f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 28 Feb 2017 12:37:06 +0100 Subject: [PATCH 338/818] adding easyconfigs: cuDNN-5.1-CUDA-8.0.44.eb --- easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb index 0cbdeea8a4..08976a1f68 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb @@ -24,7 +24,7 @@ sources = ['%(namelower)s-8.0-linux-x64-v%(version)s.tgz'] dependencies = [('CUDA', cuda_version)] checksums = [ - '099ca6a9b21b35e32f3408eff2a1c06d', # cudnn-8.0-linux-x64-v5.1.tgz + '406f4ac7f7ee8aa9e41304c143461a69', # cudnn-8.0-linux-x64-v5.1.tgz, Jan 20 2017 download ] sanity_check_paths = { -- GitLab From 1afbb4489053f466b98d4b4e1e424c14c37eb946 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 13:28:29 +0100 Subject: [PATCH 339/818] adding easyconfigs: OOMPA-3.1.2-intel-2016b-R-3.3.1.eb --- .../OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..1f054c18b4 --- /dev/null +++ b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'OOMPA' +version = '3.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://r-forge.r-project.org/projects/oompa' +description = """OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling, + and other high throughput molecular biology data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('R', '3.3.1'), + ('R-bundle-Bioconductor', '3.3', versionsuffix), +] + +ext_options = { + 'source_urls': ['http://download.r-forge.r-project.org/src/contrib/'], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# !! order of packages is important !! +exts_list = [ + ('oompaBase', '3.1.3', ext_options), + ('oompaData', '3.1.0', ext_options), + ('ClassComparison', '3.1.3', ext_options), + ('ClassDiscovery', '3.3.3', ext_options), + ('Polychrome', '0.8.1', ext_options), + ('PreProcess', '3.1.2', ext_options), + ('TailRank', '3.1.2', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' -- GitLab From dc8c67ec4f25cbd7821767e0f8392935824a5e4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 13:38:48 +0100 Subject: [PATCH 340/818] fix sanity_check_paths for OOMPA bundle --- .../easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb index 1f054c18b4..ddc58b8eb3 100644 --- a/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb +++ b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb @@ -38,7 +38,7 @@ modextrapaths = {'R_LIBS': ''} sanity_check_paths = { 'files': [], - 'dirs': [name], + 'dirs': ['ClassComparison', 'ClassDiscovery', 'oompaBase', 'oompaData', 'Polychrome', 'PreProcess', 'TailRank'], } moduleclass = 'lib' -- GitLab From 66f753fe7a49f041fb043f7a10a5ca9c601c119d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 28 Feb 2017 07:43:35 -0500 Subject: [PATCH 341/818] OpenMPI-2.*: remove --with-threads configure option. OpenMPI builds now warn they don't know --with-threads. See OpenMPI commit at https://github.com/open-mpi/ompi/commit/7a55d49ca78bcc157749c04027515f12b026ec33 sed -i 's/--with-threads=posix //' OpenMPI-2*.eb --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb | 2 +- .../OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index 23deffc8f4..e0524fac95 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.3')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index aeb2a52e4c..fe84bc7c6d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index 3d626a7c80..109e8a754d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 7d74bf0639..d395a7e376 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index c13ef6b657..171f894a0d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -15,7 +15,7 @@ checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -- GitLab From 78346f0a9a063f7adbdb3361c1eb85017d8514cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 14:28:18 +0100 Subject: [PATCH 342/818] adding easyconfigs: SpiecEasi-20160830-intel-2016b-R-3.3.1.eb --- .../SpiecEasi-20160830-intel-2016b-R-3.3.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..4b5fa1bf48 --- /dev/null +++ b/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'SpiecEasi' +version = '20160830' +commit = 'd705428' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/zdk123/SpiecEasi' +description = "Sparse InversE Covariance estimation for Ecological Association and Statistical Inference" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/zdk123/SpiecEasi/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('R', '3.3.1'), + ('R-bundle-Bioconductor', '3.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' -- GitLab From 91d00909e037c6bfb00ce16fe3a5547e2b750b94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 15:41:57 +0200 Subject: [PATCH 343/818] adding easyconfigs: iomkl-2017a.eb --- ...11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 27 +++++++++++++ .../i/imkl/imkl-2017.1.132-iompi-2017a.eb | 38 +++++++++++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 24 ++++++++++++ easybuild/easyconfigs/i/iompi/iompi-2017a.eb | 21 ++++++++++ .../n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb | 25 ++++++++++++ ....0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 33 ++++++++++++++++ 6 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2017a.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..51bcdefbaf --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['8f5fe6a9be2eb478409ad5e640b2d3ba'] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb new file mode 100644 index 0000000000..38909739c9 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iompi', 'version': '2017a'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['7911c0f777c4cb04225bf4518088939e'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb new file mode 100644 index 0000000000..442a8f32cc --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2017a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +gcc_maj_min = '6.3' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.27' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('OpenMPI', '2.0.2', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '2017.1.132', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb new file mode 100644 index 0000000000..6daa72b832 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -0,0 +1,21 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iompi' +version = '2017a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +compversuff = '-GCC-6.3.0-2.27' + +dependencies = [ + ('icc', compver, compversuff), + ('ifort', compver, compversuff), + ('OpenMPI', '2.0.2', '', ('iccifort', '%s%s' % (compver, compversuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..c6e873dfe1 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.27')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..7af5556760 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' -- GitLab From 42ce0387a380bb6e4dee94c7c46b4ed089f45097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 14:51:56 +0100 Subject: [PATCH 344/818] adding easyconfigs: randfold-2.0.1-intel-2016b.eb --- .../r/randfold/randfold-2.0.1-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb new file mode 100644 index 0000000000..e126b5aaec --- /dev/null +++ b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'randfold' +version = '2.0.1' + +homepage = 'http://bioinformatics.psb.ugent.be/software/details/Randfold' +description = "Minimum free energy of folding randomization test software" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/'] +sources = [SOURCE_TAR_GZ] + +cleanupoldinstall = False + +prebuildopts = "tar xfvz squid.tar.gz && cd squid-*/ && mkdir -p %(installdir)s && " +prebuildopts += "./configure --prefix=%(installdir)s && make && make install && cd .. && " +prebuildopts += "export CPATH=%(installdir)s/include:$CPATH && export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [(['randfold'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/randfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3267d3b1cff1437f05ae5f5452d4f4342a5419e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 14:56:09 +0100 Subject: [PATCH 345/818] clarify installing of included SQUID with comment --- easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb index e126b5aaec..9858d48447 100644 --- a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb @@ -13,6 +13,7 @@ sources = [SOURCE_TAR_GZ] cleanupoldinstall = False +# also install included SQUID dependency, since it can't be found online anymore... prebuildopts = "tar xfvz squid.tar.gz && cd squid-*/ && mkdir -p %(installdir)s && " prebuildopts += "./configure --prefix=%(installdir)s && make && make install && cd .. && " prebuildopts += "export CPATH=%(installdir)s/include:$CPATH && export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " -- GitLab From 411e66ce8fc8e34be3373f12198d99c0b84f5660 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:02:11 +0200 Subject: [PATCH 346/818] iompi uses OpenMPI not Intel MPI. Fix description --- easybuild/easyconfigs/i/iompi/iompi-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb index 6daa72b832..571b319a14 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -5,7 +5,7 @@ name = 'iompi' version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 63337dd37a65dc82da76f9ed4748b058e6bcd7bf Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:03:43 +0200 Subject: [PATCH 347/818] OpenMPI droped --with-threads configure option. See PR 4213 --- .../OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 7af5556760..0a89a8a816 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.5')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -- GitLab From 09869c2c5c361e4900492a81a806d38b9922ea5e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:04:55 +0200 Subject: [PATCH 348/818] Reduce variable setting to a minimum --- easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb index 442a8f32cc..032f6eb6a2 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -9,10 +9,7 @@ description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ a toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2017.1.132' -gcc_maj_min = '6.3' -gccver = '%s.0' % gcc_maj_min -binutilsver = '2.27' -gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +gccsuff = '-GCC-6.3.0-2.27' dependencies = [ ('icc', compver, gccsuff), -- GitLab From 9285c4116f98be71004dd3f06d564e09df489b43 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:07:47 +0200 Subject: [PATCH 349/818] Add checksum to OpenMPI config and fix style. --- .../OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 0a89a8a816..66e6aa8b1b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -8,9 +8,9 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} -sources = [SOURCELOWER_TAR_GZ] - source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -- GitLab From 0a5a3aec3cba223f4c5efe9b5200784f8f682cf8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:10:13 +0200 Subject: [PATCH 350/818] Add HPL 2.2 as test case. --- .../easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb new file mode 100644 index 0000000000..77dc4ed21f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iomkl', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 8ff202b1373c6545541888371edd6c877c92514b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 15:10:40 +0100 Subject: [PATCH 351/818] {bio}[intel/2016b] ViennaRNA v2.2.3 --- .../ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 48 +++++++++++++++++++ .../ViennaRNA-2.2.3_fix-pragma.patch | 41 ++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000..039ce2f3b3 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.2.3' + +homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] + +patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +buildopts = 'VERBOSE=1 V=1' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch new file mode 100644 index 0000000000..b53cab1fff --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch @@ -0,0 +1,41 @@ +fix #pragma statements for building with Intel compilers + +author: Kenneth Hoste (HPC-UGent) + +--- ViennaRNA-2.2.3/src/ViennaRNA/plex.c.orig 2017-02-28 14:02:21.733634118 +0100 ++++ ViennaRNA-2.2.3/src/ViennaRNA/plex.c 2017-02-28 14:02:31.303877232 +0100 +@@ -410,7 +410,7 @@ + by = (int**) vrna_alloc(sizeof(int *) * (n3+1)); + inx= (int**) vrna_alloc(sizeof(int *) * (n3+1)); + iny= (int**) vrna_alloc(sizeof(int *) * (n3+1)); +- #pragma omp ++ #pragma omp parallel for + for (i=0; i<=n3; i++){ + c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1)); + in[i] = (int *) vrna_alloc(sizeof(int) * (n4+1)); +--- ViennaRNA-2.2.3/src/Kinfold/cache.c.orig 2017-02-28 14:16:36.074432301 +0100 ++++ ViennaRNA-2.2.3/src/Kinfold/cache.c 2017-02-28 14:16:38.544493318 +0100 +@@ -56,7 +56,6 @@ + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1}; + + /* key must not be longer than 128 */ +-#pragma inline (cache_f) + unsigned cache_f(char *x) { + register char *s; + register int i; +@@ -80,6 +79,7 @@ + int cacheval; + cache_entry *c; + ++ #pragma inline (cache_f) + cacheval=cache_f(x); + if ((c=cachetab[cacheval])) + if (strcmp(c->structure,x)==0) return c; +@@ -92,6 +92,7 @@ + int cacheval; + cache_entry *c; + ++ #pragma inline (cache_f) + cacheval=cache_f(x->structure); + if ((c=cachetab[cacheval])) { + free(c->structure); -- GitLab From 7b0ef57b38446a7307e6ee02a0bc3944954327b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 15:13:00 +0100 Subject: [PATCH 352/818] adding easyconfigs: Bowtie-1.1.2-intel-2016b.eb --- .../b/Bowtie/Bowtie-1.1.2-intel-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb new file mode 100644 index 0000000000..eeada6c5ac --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb @@ -0,0 +1,23 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = [ + 'int64typedef.patch', + 'Bowtie-%(version)s_void2int.patch' +] + +moduleclass = 'bio' -- GitLab From f6ba9f30dd604bf161eb9bc3b28c9a772ecd7092 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Feb 2017 15:16:06 +0000 Subject: [PATCH 353/818] Added recipe for JasPer 2.0.10. Recent versions use CMake rather than Configure --- .../j/JasPer/JasPer-2.0.10-intel-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb new file mode 100644 index 0000000000..bf07f73dff --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.10' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +separate_build_dir = True +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib64/libjasper.so"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From c0f7edae47fa7f32c4aef11f36d23b35296b57b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 17:38:29 +0100 Subject: [PATCH 354/818] remove verbose buildopts --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 039ce2f3b3..714f3edc9e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -33,8 +33,6 @@ configopts = '--without-perl' # Code NOT yet tested, therefor left here for future recycling # preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' -buildopts = 'VERBOSE=1 V=1' - sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', -- GitLab From c4e9582b13a794b284ae9ffeccbbd3e486bab85c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:08:41 +0100 Subject: [PATCH 355/818] add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list --- .../easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 4 ++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb | 8 ++++++++ 4 files changed, 28 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb index 78af957181..f39c5f51b0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -883,6 +883,10 @@ exts_list = [ 'source_tmpl': 'Text-Template-1.46.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index dc1a3cef69..47164262e3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -881,6 +881,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb index 77e0aab0f1..3f4c7638c7 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -879,6 +879,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb index 087478fa1f..8fd86e040f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb @@ -880,6 +880,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' -- GitLab From ce9b46c84cf474d3e1c8af7c31a84cf881731cde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:11:47 +0100 Subject: [PATCH 356/818] adding easyconfigs: BLASR-2.2-intel-2016b.eb --- .../b/BLASR/BLASR-2.2-intel-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb new file mode 100644 index 0000000000..ea4423904f --- /dev/null +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'BLASR' +version = '2.2' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """ BLASR (Basic Local Alignment with Successive Refinement) rapidly maps + reads to genomes by finding the highest scoring local alignment or set of local alignments + between the read and the genome. Optimized for PacBio's extraordinarily long reads and + taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] +sources = ['smrtanalysis-%(version)s.tar.gz'] + +dependencies = [('HDF5', '1.8.18')] + +skipsteps = ['configure'] + +# the STATIC= option is a workaround. Check details here: +# https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 +buildopts = ' STATIC= ' + +installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/blasr"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 907f6bd2d2ff68a363db89ae9888a3f5dd190c34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:13:23 +0100 Subject: [PATCH 357/818] adding easyconfigs: networkx-1.1-intel-2016b-Python-2.7.12.eb --- .../networkx-1.1-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..00b1f15044 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 131240ae80a3bad7327bd8aa9d3288e31d182c87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:14:08 +0100 Subject: [PATCH 358/818] adding easyconfigs: PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb --- ...Suite-15.8.24-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8626be9af4 --- /dev/null +++ b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'PBSuite' +version = '15.8.24' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/p/pb-jelly/wiki/Home/' +description = """PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or + long 454 reads in fasta format) to high-confidence draft assembles.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://sourceforge.net/projects/pb-jelly/files/latest/download'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('networkx', '1.1', versionsuffix), + ('BLASR', '2.2'), +] + +modextrapaths = { + 'PATH': 'bin', + 'PYTHONPATH': '', +} +modextravars = {'SWEETPATH': '%(installdir)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'pbsuite'], +} + +sanity_check_commands = ["python -c 'import pbsuite'"] + +moduleclass = 'bio' -- GitLab From 650c707845c54ac8843d0a0b62ef80e2f24976a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:43:33 +0100 Subject: [PATCH 359/818] fix check for Szip library in configure script for netCDF 4.1.3 --- .../n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb | 3 +++ .../n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb | 2 ++ .../netCDF-4.1.3_fix-Szip-link-check.patch | 16 ++++++++++++++++ 3 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 6aa937d650..55b91cb833 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb @@ -5,6 +5,7 @@ homepage = 'http://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} @@ -14,6 +15,8 @@ source_urls = [ 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', ] +patches = ['netCDF-%(version)s_fix-Szip-link-check.patch'] + dependencies = [('HDF5', '1.8.7')] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index 36ab674b3d..d130575666 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -15,6 +15,8 @@ source_urls = [ 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', ] +patches = ['netCDF-%(version)s_fix-Szip-link-check.patch'] + dependencies = [ ('HDF5', '1.8.9'), ('Doxygen', '1.8.1.1'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch new file mode 100644 index 0000000000..2e44c10cb4 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch @@ -0,0 +1,16 @@ +make configure script look for correct Szip library +see also https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10433.html + +author: Kenneth Hoste (HPC-UGent) + +--- netcdf-4.1.3/configure.orig 2017-02-28 17:55:46.681729087 +0100 ++++ netcdf-4.1.3/configure 2017-02-28 17:55:52.391876458 +0100 +@@ -27142,7 +27142,7 @@ + return 0; + } + _ACEOF +-for ac_lib in '' szip; do ++for ac_lib in '' sz; do + if test -z "$ac_lib"; then + ac_res="none required" + else -- GitLab From 04873c91d34c1c9971889e9505afcfa323c2ea83 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Feb 2017 18:52:19 +0000 Subject: [PATCH 360/818] cosmetic change --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb index bf07f73dff..5bc0738e10 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -7,13 +7,14 @@ homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' description = """The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" -separate_build_dir = True toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +separate_build_dir = True + sanity_check_paths = { 'files': ["bin/jasper", "lib64/libjasper.so"], 'dirs': ["include"], -- GitLab From 98456570308e7a91e4109d0bb18bb26c05bbdf08 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Feb 2017 19:11:27 +0000 Subject: [PATCH 361/818] added cmake build dependency --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb index 5bc0738e10..23bfbfb00d 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -13,6 +13,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +builddependencies = [('CMake', '3.6.1')] + separate_build_dir = True sanity_check_paths = { -- GitLab From c341b8bbe3fe8a14a7e181d806548ca1f4b3113b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 1 Mar 2017 10:15:45 +0800 Subject: [PATCH 362/818] fix source_urls --- easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb | 3 ++- .../c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb | 3 ++- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb | 3 ++- .../i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb | 5 +++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb | 6 +++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb | 6 +++++- .../Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb | 3 ++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb | 6 +++++- easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb | 6 +++++- easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb | 6 +++++- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb | 6 +++++- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb | 6 +++++- easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb | 5 +++-- easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb | 5 +++-- easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb | 5 +++-- easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 4 +++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 4 +++- .../r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb | 4 +++- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 4 +++- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 4 +++- .../s/Subversion/Subversion-1.8.14-foss-2015a.eb | 2 ++ 35 files changed, 106 insertions(+), 42 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb index 5bba690060..85e23a5ed9 100644 --- a/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb @@ -13,8 +13,9 @@ a resource that can be and has been used in other packages.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True} -source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] +source_urls = ['http://lsbr.niams.nih.gov/bsoft/old/'] sources = ['%%(name)s%s.tar' % '_'.join(version.split('.'))] +checksums = ['e97f1fecba89efb5cd35741ce8c6396f'] cmds_map = [('.*', "./bmake omp fftw=$EBROOTFFTW")] files_to_copy = ['bin'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb index 141aedc7d3..2793fdd390 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb @@ -12,8 +12,9 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['639b86826778c14c8b1fe512f074b939'] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index c8367acc34..573a00a185 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -15,8 +15,9 @@ description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] +source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0/'] sources = [SOURCE_TAR_GZ] +checksums = ['6a2cb3f93d5e9415c74ab0f6b1ede5f0'] patches = ['EMBOSS_disable-embossupdate.patch'] diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index 88380bcbab..cfcf1c4b41 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -15,8 +15,9 @@ description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] +source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0/'] sources = [SOURCE_TAR_GZ] +checksums = ['6a2cb3f93d5e9415c74ab0f6b1ede5f0'] patches = ['EMBOSS_disable-embossupdate.patch'] diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb index 80b639f6e3..72a8492f83 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb @@ -7,8 +7,9 @@ homepage = 'http://www.gnutls.org/' description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['ffac9e22aba66057d5155ad0e3b62485'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb index bcbe21baac..9914e312e1 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb @@ -8,8 +8,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['a347a9d0f9593cf32e7555a51834f340'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb index cc86162eda..ca7cdda8cd 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb @@ -8,8 +8,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['e4ad9237f9e04e4d75e06854c55a7944'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb index 7765318123..346c8ee58b 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb @@ -8,8 +8,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['b111b2bd932c77217ad97ac8c77009fb'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb index d83125eb93..17c246342c 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb @@ -12,8 +12,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['f6a27b7996220a006720bdd82bf131be'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb index f3c4211e84..7e4fd1539e 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb @@ -12,8 +12,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['95db9b86ed542cae20634358b4924e10'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb index 5b2c252b76..36759b619b 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb @@ -17,8 +17,12 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['051c1068e6a0627f461948c365290410'] toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb index d18fddfba6..245af77e27 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb @@ -17,8 +17,12 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['051c1068e6a0627f461948c365290410'] toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb index 8175c4c179..e59823b508 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,8 @@ of any size and offers an easy and intuitive interface. toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] +checksums = ['6e90450ab3886bc650031e0d9aef367a'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb index f2baa1d123..c992ae6699 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb @@ -10,8 +10,9 @@ description = """Mercurial is a free, distributed source control management tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6e90450ab3886bc650031e0d9aef367a'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb index 43c0bceadf..4021c0012d 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb @@ -9,8 +9,9 @@ of any size and offers an easy and intuitive interface. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b467f41a262e2537cf927ed42d0fdda'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb index 47ecebdf53..1db1af42c1 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb @@ -9,8 +9,9 @@ description = """Mercurial is a free, distributed source control management tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b467f41a262e2537cf927ed42d0fdda'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb index 047324c714..af89a7e145 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb @@ -10,8 +10,9 @@ of any size and offers an easy and intuitive interface. toolchain = {'name': 'foss', 'version': '2015a'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e9447b538a101138e257d5d774bcbfb'] python = "Python" pythonversion = '2.7.9' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb index 87478cf832..8696b556c2 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['cc3bf530223e8f4aff93793b9f197bf3'] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb index a0f0b6f197..878ccb62cc 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['e7790bb23d8bc23689f19f5cec81d71e'] configopts = ['--disable-doxygen'] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb index fc24bdb27f..72e540c932 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['e7790bb23d8bc23689f19f5cec81d71e'] configopts = ['--disable-doxygen'] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb index 49f253f65d..f945f15bca 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['5eebcf19e6ac78a61c73464713cbfafc'] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb index 262ebc70b9..b162d589eb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['5eebcf19e6ac78a61c73464713cbfafc'] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb index 292fb226d3..b6ccc91bd2 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -16,8 +16,9 @@ description = """ pigz, which stands for parallel implementation of gzip, is a f toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://zlib.net/pigz/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a41409da23ff093b61e414d602c5650'] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb index 770c70dd5f..e3e7f189b1 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb @@ -16,8 +16,9 @@ description = """ pigz, which stands for parallel implementation of gzip, is a f toolchain = {'name': 'ictce', 'version': '6.2.5'} -source_urls = ['http://zlib.net/pigz/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a41409da23ff093b61e414d602c5650'] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb index e95cb85cb9..a50f50774e 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb @@ -16,8 +16,9 @@ description = """ pigz, which stands for parallel implementation of gzip, is a f toolchain = {'name': 'foss', 'version': '2015b'} -source_urls = ['http://zlib.net/pigz/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fb80e8d31498226c99fe8c8b3d19364d'] # Patch Makefile so zlib provided by EasyBuild is picked up patches = ['pigz-2.3.3_Makefile.patch'] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb old mode 100755 new mode 100644 index 9a78780f34..a2bf4ab035 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['e60d1a896299d000b6a34f032debc9aa'] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb index 4e14ff0190..f56b457e0d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['114ea7f18b48ed0b3bb0287f5a6d593f'] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index a65a733278..a263fbc4af 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['114ea7f18b48ed0b3bb0287f5a6d593f'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-%(version)s_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb index e025c77b02..4f55d64d72 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['3124168ce6b4574b471d6cda4aa40184'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index f0e1274759..a8ab1f540d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['2a9ef6a342833cb461020fa0832e78fe'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 05baffbd16..5801dbe265 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['aa90309fa75ab69816dc819f5edd73f5'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb index eb76e73818..81b811dc89 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['fd9ee9cfc85cdad3d7c2c41a28796c24'] + patches = [ 'configure_FftwFromMkl_28.patch', ] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index fc6f18713c..9dd615415d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['fd9ee9cfc85cdad3d7c2c41a28796c24'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index 7d1106317b..b51c955db4 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['6a1ad549b3b79b10bbb1f116b49067ee'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb index be6f1332e2..cf172a3cf0 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -12,8 +12,10 @@ source_urls = [ 'http://apache.belnet.be/%(namelower)s', 'http://www.eu.apache.org/dist/%(namelower)s', 'http://www.us.apache.org/dist/%(namelower)s', + 'http://archive.apache.org/dist/%(namelower)s', ] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['fe476ba26d6835eba4393780ea907361'] dependencies = [ ('APR', '1.5.2'), -- GitLab From 17ebe626b0f62265d4275423bddaad96c00bbfb7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 Mar 2017 09:27:13 +0200 Subject: [PATCH 363/818] adding easyconfigs: Python-2.7.12-iomkl-2017a.eb --- .../g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb | 31 ++++ .../l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb | 27 ++++ .../libreadline-6.3-GCCcore-6.3.0.eb | 33 +++++ .../p/Python/Python-2.7.12-iomkl-2017a.eb | 133 ++++++++++++++++++ .../s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb | 44 ++++++ .../t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb | 30 ++++ .../t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb | 30 ++++ .../z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb | 27 ++++ 8 files changed, 355 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2d442cdea2 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.1' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('binutils', '2.27'), + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..ab5a66564f --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.27'), +] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f4f4e99acd --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +builddependencies = [('binutils', '2.27')] +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb new file mode 100644 index 0000000000..47c4558b9f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.12' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iomkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.24', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.5.3', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f7ba78e654 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..3d473ebedb --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..0c78137460 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..5c5b309e90 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [ + ('binutils', '2.27', '', True) +] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From a9ee6588e0281da234489af8df025bc1ad605b3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 09:13:45 +0100 Subject: [PATCH 364/818] adding easyconfigs: miRDeep2-2.0.0.8-intel-2016b.eb --- .../miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb new file mode 100644 index 0000000000..1a5f00c298 --- /dev/null +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'miRDeep2' +version = '2.0.0.8' +altver = '_'.join(version.split('.')) + +homepage = 'https://www.mdc-berlin.de/8551903/en/' +description = "miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs" + +source_urls = ['https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/'] +sources = ['mirdeep%s.zip' % altver] + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('Perl', '5.24.0'), # provides PDF::API2 + ('Bowtie', '1.1.2'), + ('ViennaRNA', '2.2.3'), + ('randfold', '2.0.1'), # also provides SQUID +] + +install_cmd = "cp -a mirdeep%s/src %%(installdir)s/bin" % altver + +sanity_check_paths = { + 'files': ['bin/make_html.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From b61226296efcb1e72e351e595841a25d4a066632 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 09:56:15 +0100 Subject: [PATCH 365/818] fix style remarks in miRDeep2 easyconfig --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 1a5f00c298..583f9a91f7 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -7,11 +7,12 @@ altver = '_'.join(version.split('.')) homepage = 'https://www.mdc-berlin.de/8551903/en/' description = "miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs" -source_urls = ['https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/'] -sources = ['mirdeep%s.zip' % altver] - toolchain = {'name': 'intel', 'version': '2016b'} +source_url_subdir = 'research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/' +source_urls = ['https://www.mdc-berlin.de/45995549/en/' + source_url_subdir] +sources = ['mirdeep%s.zip' % altver] + dependencies = [ ('Perl', '5.24.0'), # provides PDF::API2 ('Bowtie', '1.1.2'), -- GitLab From cbaba10168bd2b27c854f848df7fbcbe1d628e88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 10:18:54 +0100 Subject: [PATCH 366/818] fix source spec in PBSuite easyconfig --- .../p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb index 8626be9af4..c6a303fc3e 100644 --- a/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb @@ -11,7 +11,7 @@ description = """PBJelly is a highly automated pipeline that aligns long sequenc toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://sourceforge.net/projects/pb-jelly/files/latest/download'] -sources = ['%(name)s_%(version)s.tar.gz'] +sources = ['%(name)s_%(version)s.tgz'] dependencies = [ ('Python', '2.7.12'), -- GitLab From 0713ba2281954b4626ad750a98c0a6183a14093e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 Mar 2017 13:21:20 +0200 Subject: [PATCH 367/818] adding easyconfigs: NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb --- ...46-iomkl-2017a-2015-10-20-Python-2.7.12.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb new file mode 100644 index 0000000000..f693ccc152 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb @@ -0,0 +1,38 @@ +name = 'NWChem' +version = '6.6.revision27746' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'iomkl', 'version': '2017a'} +toolchainopts = {'i8': True} + +source_urls = ['http://www.nwchem-sw.org/download.php?f='] +verdate = '2015-10-20' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.12' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +# This easyconfig is using the default for armci_network (OPENIB) and +# thus needs infiniband libraries. +osdependencies = [ + ('libibverbs-dev', 'libibverbs-devel'), + ('libibumad-dev', 'libibumad-devel'), +] + +modules = 'all python' + +moduleclass = 'chem' -- GitLab From 26a826ec08b3b3769ff03ae5179c0c71739a7b39 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 Mar 2017 17:54:11 +0200 Subject: [PATCH 368/818] Add missing patch file. --- ...Chem-6.6.revision27746-parallelbuild.patch | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch new file mode 100644 index 0000000000..635f15ee4c --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch @@ -0,0 +1,80 @@ +diff -ru nwchem-6.6.orig/src/config/makefile.h nwchem-6.6/src/config/makefile.h +--- nwchem-6.6.orig/src/config/makefile.h 2015-10-16 02:12:50.000000000 +0200 ++++ nwchem-6.6/src/config/makefile.h 2017-01-12 10:43:00.000000000 +0100 +@@ -958,7 +958,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w -g + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1163,7 +1163,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1310,7 +1310,7 @@ + _FC=ifc + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w -g + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1372,7 +1372,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w -g + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII +@@ -1740,7 +1740,7 @@ + # only use EXPLICITF for offload because otherwise we want debugging to be easy + # FOPTIONS += -Qoption,fpp,-P -Qoption,fpp,-c_com=no -allow nofpp_comments + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + #to avoid compiler crashes on simd directive. e.g .Version 15.0.2.164 Build 20150121 + ifdef USE_NOSIMD +@@ -1748,7 +1748,6 @@ + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + else +@@ -1759,10 +1758,9 @@ + endif + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -1885,10 +1883,9 @@ + COPTIONS += -qopt-report-phase:openmp + endif + else +- COPTIONS += -vec-report=1 + ifdef USE_OPENMP + COPTIONS += -openmp +- COPTIONS += -openmp-report=2 ++ COPTIONS += -openmp-report=0 + endif + endif + COPTIMIZE = -O3 -- GitLab From 1401b818611d041a21eae310aa329bc03e1b0788 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:31:11 +0100 Subject: [PATCH 369/818] fx style issues in pscom easyconfigs --- easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb | 4 ++-- easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb | 4 +++- .../p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb | 6 ++++-- easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb | 6 ++++-- 4 files changed, 13 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb index 65a73afe7d..147a4add74 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb @@ -4,8 +4,8 @@ name = 'pscom' version = '5.0.43' homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting -of a high-performance communication layer (MPI) and a sophisticated management layer.""" +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb index b69d0d92dd..0b3259fa6d 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb @@ -3,7 +3,9 @@ easyblock = 'ConfigureMake' name = 'pscom' version = '5.0.44-1' homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" + toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb index 7da1e4a7f7..af331b28c2 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb @@ -2,10 +2,12 @@ easyblock = 'ConfigureMake' name = 'pscom' version = '5.0.44-1' + homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" -toolchain = {'name': 'iccifort', 'version': '2015.1.133'} +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" +toolchain = {'name': 'iccifort', 'version': '2015.1.133'} source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] sources = ['%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb index 13b9a47c54..fc283ffce3 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb @@ -4,7 +4,8 @@ name = 'pscom' version = '5.0.48-1' homepage = 'http://www.par-tec.com' -description = "ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer." +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" toolchain = {'version': '', 'name': 'dummy'} @@ -16,7 +17,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['include/%(name)s.h', ('lib/libpscom.so', 'lib64/libpscom.so'), ('lib/libpscom4mxm.so', 'lib64/libpscom4mxm.so')], + 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT), + ('lib/libpscom4mxm.%s' % SHLIB_EXT, 'lib64/libpscom4mxm.%s' % SHLIB_EXT)], 'dirs': [], } -- GitLab From 5357919d46ac26b8e6d0cfe0025c6502725bb75a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:32:41 +0100 Subject: [PATCH 370/818] fix whitespace issues & long lines --- .../pyplusplus-20160707-foss-2016a-Python-2.7.11.eb | 1 - .../pyplusplus-20160707-foss-2016a-Python-3.5.1.eb | 1 - .../python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 8 ++++---- easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb | 4 ++-- 7 files changed, 12 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb index 695617390c..8ebd6c8d2e 100644 --- a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb @@ -32,4 +32,3 @@ sanity_check_paths = { options = {'modulename': '%(name)s'} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb index 98760a6c19..b72f894f40 100644 --- a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb @@ -30,4 +30,3 @@ sanity_check_paths = { options = {'modulename': '%(name)s'} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb index 9f1bdc61f3..1f3dfbd69d 100644 --- a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,8 @@ name = "python-dateutil" version = "2.1" homepage = "https://pypi.python.org/pypi/python-dateutil" -description = """The dateutil module provides powerful extensions to the datetime module available in the Python standard library.""" +description = """The dateutil module provides powerful extensions to the datetime module available + in the Python standard library.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index eacf9a8384..48881e75e8 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -6,11 +6,11 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] -sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] +source_urls = ['http://download.qt.io/official_releases/qt/4.8/%(version)s'] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.gz'] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' -configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' platform = 'linux-g++-64' moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb index e773ad310a..f091886679 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb @@ -22,8 +22,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', - 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], 'dirs': ['bin/samtools-1.3'], } diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb index 5420a22996..85267f0972 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb @@ -22,8 +22,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', - 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], 'dirs': ['bin/samtools-1.3'], } diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb index d01f2f9089..e70842c9f5 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb @@ -24,8 +24,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', - 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], 'dirs': ['bin/samtools-1.3'], } -- GitLab From 623dbaebd8e171c358eb6d245bc48c317ce82d3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:35:19 +0100 Subject: [PATCH 371/818] fix long lines in RAxML easyconfigs --- .../r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb | 3 ++- .../r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb | 3 ++- 16 files changed, 32 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb index 985c883441..1eb4b3b846 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb index e09f71abf5..7004dce41e 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb index 0fe0530f3a..d7300ce6e9 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb index af08c5c5e5..ee4a21ba93 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb index 0868a2b38e..fe4066ef14 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb index 3a1597463c..fbae2547b2 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb index 153acb7424..c9087e258f 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb index e7ee2daf46..fdc9f97544 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb index d053b3dc21..1c1435652c 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb index 575001db8d..0ccbb936e8 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb index a1fec5b741..dc772a459b 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb index f253cc9c29..caffbdd4c7 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb index 7eb0b37f64..05f29e6aa6 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb index 0058765fc5..25dd91ac1d 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb index 86dab359ac..eef4968327 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb index b107d2a11a..89cf1e0f0b 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], -- GitLab From 611c237d3dc0b2e4cce6aeee05b9647b156792fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:57:08 +0100 Subject: [PATCH 372/818] trivial whitespace fixes --- easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb | 2 +- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- .../protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb | 2 +- .../protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 2 +- .../protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb | 2 +- .../protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb | 2 +- .../protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb | 2 +- .../protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb | 2 +- 18 files changed, 18 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb index 9407a6399e..8a34ad1f5e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb @@ -13,6 +13,6 @@ source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor) sources = ['%(namelower)s_%(version)s_linux-run'] -modextravars = { 'CUDA_HOME': '%(installdir)s' } +modextravars = {'CUDA_HOME': '%(installdir)s'} moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index e1484d4027..4a545a7291 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -44,7 +44,7 @@ dependencies = [ configopts = '-DBLAS=open' -modextrapaths = {'PYTHONPATH': ['python'] } +modextrapaths = {'PYTHONPATH': ['python']} sanity_check_paths = { 'files': ['bin/caffe'] + diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb index 69c610cd3f..94b4d8c173 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '2.8.10.2')] sanity_check_paths = { 'files': ["lib/libfreexl.la"], 'dirs': ["lib"] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb index 0401395acc..e2833c7203 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.2.2')] sanity_check_paths = { 'files': ["lib/libfreexl.la"], 'dirs': ["lib"] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb index c38933ad4f..40bff9f910 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.4.1')] sanity_check_paths = { 'files': ["lib/libfreexl.la"], 'dirs': ["lib"] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb index 7b11ad3065..2e9b594a70 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.7.1')] sanity_check_paths = { 'files': ['lib/libfreexl.a'], 'dirs': [] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 681a2da8cf..66efa1aea5 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = {'IMINTASSERDB': '/path/to/databases/I-TASSER/%(version)s'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb index 986362ad06..3027748d68 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb index fbb897d434..fb8104961b 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb index 8512c8ff8b..1f800a9ecb 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb index c25cad0fae..14ca314505 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb index 2dd5db9c4e..fd34141ef9 100755 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb index fa54b7dce0..51988758fd 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb index de900f73b2..01689413cc 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb index 58f5db7a33..2c00792f81 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb index 9daa7bba81..ab2a54c1b6 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb index ec75812a65..8b079f0d60 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb index 20e9ee0821..8986e89a6d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From 6382f6cedc8f53da4f823ca5ed5e545ac5967c0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:06:40 +0100 Subject: [PATCH 373/818] sync commented out OpenSSL specs in Python easyconfigs --- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 4 +++- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 4 +++- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 5 +++-- .../p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 5 +++-- .../p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb | 5 +++-- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb | 4 +++- 40 files changed, 120 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ace4711442..bbbadf3e32 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index b1bdb4f782..c5675d8144 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index cc84b14111..9cb0c165c6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index f325e4238c..0cacb5b908 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 1ba18083e7..c4b91910db 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index e615c89354..6cb74160de 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 7d445cd6ba..2bf2b3c0c7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.7.2')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index 55f10df08f..d616f3a678 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.8.4')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 017e1ecaae..3bba96e78d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 276aa8a0f3..5578abe094 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb index 78953148b0..7248257795 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index c5fe86070e..7ca3e0d30a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.10.0'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # required for pycrypto - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index cd19e3b902..90aff56172 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 917a362739..540888954b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index fa2f05cdb9..66287172c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index 914f184b70..49ed840807 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 8b707bfd80..4fa82a32c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -25,8 +25,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', versionsuffix), ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 711240b058..36a33282cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index bb77d83c1d..9cf2d30627 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 0cda45ec7d..0d7187668b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 4ef1bfeaeb..1f04581f6c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 12a347ef6d..d6acb56cd0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 6265b2329d..0a6a82b9fe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index a22416f124..78b8331206 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index d9a96be894..8bc486f394 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -21,7 +21,9 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('SQLite', '3.8.5'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 48e0894d30..f91d5d9be1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index e6e366e13c..1589ad3044 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 384ccabeee..cc438001ba 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 91008ef87d..8a3b97a885 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 9f687fe594..ff8c4dd1f7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 5f8e6aeeb0..400936afa7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 95e0f82630..535df5f445 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -26,7 +26,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 18384a6b3c..15167c0da9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index dc5adffe37..5da8fad6cd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index e164d75eb8..530b345146 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 7fc679ddfb..1f4aa039b5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 5b5ea68742..d79d72ab00 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index 8ba5022eb1..cacde6a179 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -22,7 +22,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 948d875463..85a061b4b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index db1c3e7576..43f98bbf39 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From 9177dc08613b45e38b6ae052fd1f0ff3cf3d493c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:07:08 +0100 Subject: [PATCH 374/818] fix more long lines --- .../p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 4 +++- .../p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb | 3 ++- .../prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb | 3 ++- .../prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb | 3 ++- .../prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb | 3 ++- .../prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb | 3 ++- .../prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb | 3 ++- 10 files changed, 20 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 67abbe4783..ba44c00e4e 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,9 @@ name = 'paycheck' version = '1.0.2' homepage = 'https://pypi.python.org/pypi/paycheck/' -description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" +description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of + QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, + rather than testing its results for a given input.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 9fdde70731..bead17f746 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'paycheck' version = '1.0.2' homepage = 'https://pypi.python.org/pypi/paycheck/' -description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. - PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" +description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of + QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, + rather than testing its results for a given input.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb index 0387cd385f..f2d716e0cd 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = "petsc4py" version = "3.3" homepage = 'https://code.google.com/p/petsc4py/' -description = """petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.""" +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb index 50d6cb2145..d31fcf86b6 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,7 @@ name = "petsc4py" version = "3.3" homepage = 'https://code.google.com/p/petsc4py/' -description = """petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.""" - +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb index 0dc0fbea27..035c739fdd 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,8 @@ version = '1.0.13' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb index fe4231de3b..4c956fc8b1 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb @@ -5,7 +5,8 @@ version = '1.0.3' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb index 4b1aefd0e6..83eb4807ee 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb @@ -5,7 +5,8 @@ version = '1.0.3' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb index e6261f564a..7ba652badd 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb @@ -5,7 +5,8 @@ version = '1.0.6' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb index a4fd060e9c..dc44707f0f 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,8 @@ version = '1.0.6' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb index 6c89475fe0..1e7549ab87 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb @@ -5,7 +5,8 @@ version = '1.0.6' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'intel', 'version': '2016b'} -- GitLab From d0561aeac63524671642b317cfbe1135932606d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:16:17 +0100 Subject: [PATCH 375/818] fix long lines in ParMETIS easyconfigs --- .../p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb | 11 +++++------ .../p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb | 11 +++++------ .../p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb | 10 +++++----- 14 files changed, 70 insertions(+), 72 deletions(-) diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb index 8183de649d..c1a6599161 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '3.1.1' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb index 11db9fe038..f11fa30bf5 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb @@ -2,12 +2,11 @@ name = 'ParMETIS' version = '3.1.1' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" - +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb index 5223c55c4b..da4fa31fda 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '3.2.0' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb index d331f06b60..0becabf505 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '3.2.0' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb index f4413be294..36ec81e338 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.2' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb index a32790b7f1..e92565e46a 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb @@ -2,12 +2,11 @@ name = 'ParMETIS' version = '4.0.2' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" - +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb index 6134d068c9..cbbcc0a04a 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb index c7f412f769..6ed756b305 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb index ebbc3db5a2..18b94b4475 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb index db08a4e643..07bf0cde29 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb index 1521fb5934..f8d63fb067 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb index 9212c66919..c2177256c3 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb index 3487dd6842..b323ea3886 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb index d1d34fb057..ddb7b34451 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': True, 'pic': True} -- GitLab From 99a05b9a1f4f368a50b3f7e054a57b733283f151 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:35:09 +0100 Subject: [PATCH 376/818] fix long lines in PSI easyconfigs --- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb | 3 ++- .../p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb | 3 ++- 7 files changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb index 528a6728be..33bdd4e669 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb @@ -17,7 +17,8 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb index 674a15f04b..300abe34c8 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb @@ -15,7 +15,8 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb index c680330c40..a35b218f7d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb @@ -18,7 +18,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb index 288d0bd7ab..6444ef03e0 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb @@ -17,7 +17,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb index e65fbf7805..d50c1e4431 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb @@ -18,7 +18,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb index 7be55fa034..d969aa2c91 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb @@ -17,7 +17,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb index e299f3c676..c3469f5c4d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -19,7 +19,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' -- GitLab From f4d0a3ef2d2040908622d886f7ed6b717caae073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:35:26 +0100 Subject: [PATCH 377/818] minor style fixes in PSORTb and Pasha easyconfigs --- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index b5baf3a55c..99940a8a08 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -31,7 +31,7 @@ preconfigopts = "export PSORTROOT=%(installdir)s && " prebuildopts = 'sed -i "s/CC = cc/CC ?= gcc/" bio-tools-psort-modhmm/Makefile && ' postinstallcmds = [ - "cp -r psort/* %(installdir)s/.", + "cp -r psort/* %(installdir)s/.", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index a72485e97d..161ca2d383 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -15,8 +15,8 @@ sources = [SOURCE_TAR_GZ] patches = [ 'intelmpi.patch', - # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version of libstdc++ - # since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. + # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version + # of libstdc++ since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. 'old-libstdc++-hash_fun-map-set_pasha-1.0.5.patch', ] -- GitLab From 51157b17a08bfb23ba488cf7144eb84bd73e3146 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 22:21:15 +0100 Subject: [PATCH 378/818] moar style fixes in various easyconfigs --- .../c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb | 2 +- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- .../easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb | 2 +- .../easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb | 5 +++-- .../o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 8 +++----- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 4 ++-- .../o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 4 ++-- easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 4 ++-- easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb | 4 ++-- .../o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 8 ++++---- .../o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 4 ++-- .../o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb | 4 ++-- .../OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- .../OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 4 ++-- .../PCMSolver-20160205-intel-2016a-Python-2.7.11.eb | 3 ++- easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb | 2 +- .../p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb | 5 ++--- .../p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb | 4 ++-- easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb | 3 +-- easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb | 4 ++-- .../easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb | 4 ++-- .../PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb | 2 -- 31 files changed, 54 insertions(+), 60 deletions(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index edd7b1aa5d..2db5248504 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -28,7 +28,7 @@ modextrapaths = { sanity_check_paths = { 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", - "bin_rh_linux64/wb_view",], + "bin_rh_linux64/wb_view"], 'dirs': ["resources"] } diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 0d8dbcbf47..6706bb83e5 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -21,7 +21,7 @@ dependencies = [ builddependencies = [('Bison', '2.5')] -osdependencies = [('libcr-dev', 'blcr-devel'),] +osdependencies = [('libcr-dev', 'blcr-devel')] # enable building of MPE routines withmpe = True diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb index a33090c4b6..81fb2b9ec4 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb index c9ebfcb9f5..127aea160a 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb index 52365b33f3..126cbec2e8 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb @@ -26,9 +26,10 @@ builddependencies = [ ] # make sure both static and shared libs are built +common_configopts = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s -DCURL_INCLUDE_DIR=$EBROOTCURL/include" % SHLIB_EXT configopts = [ - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON" % SHLIB_EXT, - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF" % SHLIB_EXT, + common_configopts + " -DBUILD_SHARED_LIBS=ON", + common_configopts + " -DBUILD_SHARED_LIBS=OFF", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index fbe8f5cfab..84d9f1db9a 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -5,17 +5,15 @@ version = '1.2.9' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' -description = """ The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using - the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of - commands using the pipe mecanism. -""" +description = """The OBITools programs aims to help you to manipulate various data and sequence files in a + convenient way using the Unix command line interface. They follow the standard Unix interface for command line + program, allowing to chain a set of commands using the pipe mecanism. """ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), ('Cython', '0.24.1', versionsuffix), diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index a85c46d3f0..95182fb7f6 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -30,8 +30,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 685a061dbd..a2fb635e48 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -32,8 +32,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index 7d27755495..9cd49048ac 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -31,8 +31,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index 6a633a98ef..82c2d0b54b 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -31,8 +31,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index e3cd54d745..26fbd9394a 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'usempi': True, 'opt': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/' ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/'] builddependencies = [ ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 0292e9d416..1495f695f6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # the hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -40,7 +40,7 @@ dependencies = [ ('GTK+', '2.24.31'), ] -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# the destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) @@ -65,8 +65,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb index ac26d4212f..422607a28b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.3')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb index af22c5f516..ded2f408ed 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.3')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index e0524fac95..ced6423707 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '5.2.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.3')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] # VampirTrace is no longer used : https://www.open-mpi.org/community/lists/announce/2016/07/0085.php libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index fe84bc7c6d..dccf9a16b7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index 109e8a754d..bc5a7af11f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gcccuda', 'version': '2016.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index d395a7e376..79bff619c0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 171f894a0d..3e05777f37 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -21,7 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 66e6aa8b1b..b2aa187ae0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -8,7 +8,7 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['886698becc5bea8c151c0af2074b8392'] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb index 861cd9d963..945b858a59 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb @@ -27,7 +27,8 @@ builddependencies = [ ('Eigen', '3.2.7'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN -DCMAKE_CXX_FLAGS="$LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' +configopts = "-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN " +configopts += '-DCMAKE_CXX_FLAGS="$LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' separate_build_dir = True diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 03cdf3c1c3..12016d01cb 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -22,4 +22,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb index 56139c42c1..f00e26a484 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb @@ -3,8 +3,8 @@ version = "3.3-p2" versionsuffix = '-Python-2.7.3' homepage = 'http://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution -of scientific applications modeled by partial differential equations.""" +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb index 193d113315..deb2a22bc2 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb @@ -3,9 +3,8 @@ version = "3.3-p2" versionsuffix = '-Python-2.7.3' homepage = 'http://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution - of scientific applications modeled by partial differential equations.""" - +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb index 72b0ef23a9..15e5de651c 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb @@ -3,8 +3,8 @@ version = "3.5.1" versionsuffix = '-Python-2.7.8' homepage = 'http://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution - of scientific applications modeled by partial differential equations.""" +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb index 49864adcd3..099d8a684a 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb @@ -19,7 +19,6 @@ dependencies = [ ] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb index d3260f31f8..4414621a52 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb @@ -15,7 +15,6 @@ versionsuffix = '-%s-%s' % (gnu, gnuver) dependencies = [(gnu, gnuver)] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb index 6589eba972..f9744db69b 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb @@ -15,7 +15,6 @@ versionsuffix = '-%s-%s' % (gnu, gnuver) dependencies = [(gnu, gnuver)] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb index 90aea78df7..6ded928e61 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb @@ -16,8 +16,8 @@ buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] sanity_check_paths = { - 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], - 'dirs': ['bin'], + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb index 312062d04f..8fca37e015 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb @@ -16,8 +16,8 @@ buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] sanity_check_paths = { - 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], - 'dirs': ['bin'], + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb index 3f257ab0c1..ffd93ce336 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb @@ -42,6 +42,4 @@ configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' # Execute 4 tests in parallel runtest = 'ARGS="-V -E \'opt10|pubchem1|pubchem2|pywrap-opt-sowreap|sapt4\' -j 4" test' - - moduleclass = 'chem' -- GitLab From 8f5214c969da42a82a783c5782dc13432600647c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 22:27:24 +0100 Subject: [PATCH 379/818] fix style fixes in ConnectomeWorkbench easyconfig --- .../c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index 2db5248504..fce250c7cf 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -21,9 +21,9 @@ source_urls = ['https://ftp.humanconnectome.org/workbench/'] sources = ['workbench-rh_linux64-v%(version)s.zip'] modextrapaths = { - 'PATH': 'bin_rh_linux64', - 'LIBRARY_PATH': 'libs_rh_linux64', - 'LD_LIBRARY_PATH': 'libs_rh_linux64', + 'PATH': 'bin_rh_linux64', + 'LIBRARY_PATH': 'libs_rh_linux64', + 'LD_LIBRARY_PATH': 'libs_rh_linux64', } sanity_check_paths = { @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 32a7e256f1753eb22ef21a3eebe466a03106e429 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 2 Mar 2017 14:04:48 +0800 Subject: [PATCH 380/818] prepare release notes for eb311 --- RELEASE_NOTES | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a240d6d9d8..aa222f795f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,55 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.1 (March 3rd 2017) +----------------------- + +bugfix release +- added example easyconfig files for 15 new software packages: + - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), + meshio (#4178), miRDeep2 (#4229), OOMPA (#4211), PBSuite (#4230), randfold (#4217), Smoldyn (#4110), + SpiecEasi (#4215), stress (#4180) +- added additional easyconfigs for various supported software packages, including: + - ATK 2.22.0, Armadillo 7.600.2 + 7.800.0, arpack-ng 3.4.0, BLASR 2.2, Bazel 0.4.4, BioPerl 1.7.1, CFITSIO 3.41, + CGAL 4.9, CMake 3.7.2, Cantera 2.3.0, cURL 7.52.1, DMTCP 2.5.0, Eigen 3.2.10 + 3.3.2 + 3.3.3, Emacs 25.1, + ea-utils 1.04.807, freetype 2.7.1, GMP 6.1.2, Graphviz 2.38.0, gettext 0.19.8.1, IPython 5.2.2, JasPer 2.0.10, + Java 1.8.0_121, Lmod 7.3, libQGLViewer 2.6.4, libpng 1.6.27 + 1.6.28, likwid 4.2.0, MCL 02.063 + 14.137, + MCR R2013b + 2014b + R2015b + R2016b, matplotlib 2.0.0, networkx 1.1, OpenSSL 1.1.0e, OrthoMCL 1.4 + 2.0.9, + PCRE 8.40, PyTables 3.2.3.1, Pysam 0.10.0, path.py 10.1, prompt-toolkit 1.0.13, Qt5 5.8.0, ROOT 6.06.02, + SCons 2.5.1, Stacks 1.44, StringTie 1.3.3, sickle 1.33, VTK 7.1.0, ViennaRNA 2.2.3, Vim 8.0, XZ 5.2.3, + Yade 2017.01a +- added easyconfigs for new 'iomkl/2017a' and 'iompi/2017a' toolchains (#4216) +- various enhancements, including: + - clean up dependencies in libdrm (#4113) + - update X11 bundle and dependencies for GCCcore-6.3.0 (#4147) + - fix style in several easyconfigs (#4174, #4176, #4190) +- various bug fixes, including: + - allow intel 2017 to compile (#4102) + - work around build failure with GCC 6 in pkg-config (#4109) + - add Bison and gettext as build deps for X11 (#4111) + - fix ippicv source download and library install in OpenCV (#4126) + - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4135) + - get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146) + - remove duplicate sources specification in OpenMPI (#4150) + - fix definition of buildopts/installopts in Cantera easyconfig (#4164) + - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) + - fix broken test in Cantera 2.3.0 rather than skipping it (#4177) + - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) + - update $PATH in OrthoMCL 1.4 easyconfig (#4182) + - bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a (#4188) + - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) + - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) + - set CMAKE_PREFIX_PATH to ncurses install directory (#4196) + - switch to lowopt=True for libxc v2.2.* and v3.* (#4199) + - remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200) + - fix version (& homepage) in ea-utils easyconfigs (#4205) + - remove --with-threads configure option in OpenMPI-2.* (#4213) + - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) + - fix check for Szip library in configure script for netCDF 4.1.3 (#4226) +- fix source_urls in several easyconfigs, including: + - bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227) + + v3.1.0 (February 3rd 2017) -------------------------- -- GitLab From d6b4285dafcac0f505cfaf93a50910dbe5fe9d54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 Mar 2017 08:45:24 +0200 Subject: [PATCH 381/818] Add comment to patch file with author and purpose. --- .../n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch index 635f15ee4c..5d07c595e7 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch @@ -1,3 +1,5 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 diff -ru nwchem-6.6.orig/src/config/makefile.h nwchem-6.6/src/config/makefile.h --- nwchem-6.6.orig/src/config/makefile.h 2015-10-16 02:12:50.000000000 +0200 +++ nwchem-6.6/src/config/makefile.h 2017-01-12 10:43:00.000000000 +0100 -- GitLab From 8a3f307ee6250f5d70eca2788292014cb1f2c0c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 09:08:52 +0100 Subject: [PATCH 382/818] restore original fftw version in NFFT dep spec --- easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb index 127aea160a..4df5eead7f 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] sanity_check_paths = { -- GitLab From b5944e17d62f4cb5a45938768639b2138c9b0f52 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 09:46:45 +0100 Subject: [PATCH 383/818] remove single space at the end of OBITools description to make @wpoely86 happy --- .../o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index 84d9f1db9a..82a7c41aa7 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' description = """The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using the Unix command line interface. They follow the standard Unix interface for command line - program, allowing to chain a set of commands using the pipe mecanism. """ + program, allowing to chain a set of commands using the pipe mecanism.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From 05ffcaa5c995fd346fa6b373b604412834c14637 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 2 Mar 2017 11:47:37 +0100 Subject: [PATCH 384/818] fix missing PYTHONPATH --- .../r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb index 81755cd856..6bb0455477 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -42,4 +42,6 @@ configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' configopts += '-Dcxx14=ON ' configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 97c578af87d9a9e16dd112cb980d70451d127f0a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 2 Mar 2017 13:35:05 +0100 Subject: [PATCH 385/818] rootpy-foss-2016a-python-2.7.11 --- .../rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a81bc6e8ba --- /dev/null +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'rootpy' +version = '0.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.rootpy.org/' + +description = """The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with +ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to +improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a +multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface +between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate +your data and to take advantage of these alternatives if needed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), + ('ROOT','v6.08.02','-Python-%(pyver)s'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s') +] + +options = {'modulename': 'os'} + +#sanity_check_paths = { +# 'files': ['bin/quast.py'], +# 'dirs': [''], +#} + +moduleclass = 'bio' -- GitLab From 0853a413d724c2ae3d24353a42abaf97d635f6f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 2 Mar 2017 16:30:31 +0100 Subject: [PATCH 386/818] add tmux-2.3 --- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 26 ++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.3.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb new file mode 100644 index 0000000000..d9aa356199 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.3' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.1.8'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 66e53395be9c6c3a6e823fa9066ae6f810fff67c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 2 Mar 2017 16:40:48 +0100 Subject: [PATCH 387/818] add libevent-2.1.8.eb --- .../easyconfigs/l/libevent/libevent-2.1.8.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb new file mode 100644 index 0000000000..964ec6943d --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +moduleclass = 'lib' -- GitLab From e61539844a7930b15d93f805c7e1cbd08a8ac3d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 19:13:20 +0100 Subject: [PATCH 388/818] adding easyconfigs: evmix-2.6-intel-2016b-R-3.3.1.eb --- .../e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..9999a81cbc --- /dev/null +++ b/easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'evmix' +version = '2.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://cran.r-project.org/web/packages/evmix' +description = """evmix: Extreme Value Mixture Modelling, + Threshold Estimation and Boundary Corrected Kernel Density Estimation""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('R', '3.3.1'), + ('GSL', '2.3'), +] + +exts_defaultclass = 'RPackage' +exts_list = [ + ('gsl', '1.9-10.3', { + 'source_urls': ['http://cran.r-project.org/src/contrib/'], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + }), + ('evmix', '2.6', { + 'source_urls': ['http://cran.r-project.org/src/contrib/'], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['evmix', 'gsl'], +} + +modextrapaths = {'R_LIBS': ['']} + +moduleclass = 'math' -- GitLab From 49d9583a535d924354c98f91e191e05181f49f65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 19:18:23 +0100 Subject: [PATCH 389/818] adding easyconfigs: skewer-0.2.2-intel-2016b.eb --- .../s/skewer/skewer-0.2.2-intel-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb new file mode 100644 index 0000000000..c70dfa11d6 --- /dev/null +++ b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'skewer' +version = '0.2.2' + +homepage = 'https://github.com/relipmoc/skewer' +description = """skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter + trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/relipmoc/skewer/archive'] +sources = ['%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX" CXXFLAGS="-c $CXXFLAGS" LDFLAGS="$CXXFLAGS -pthread"' + +files_to_copy = [(['skewer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skewer'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6df11f2f4600f8c84f81590c50c447963b08eae5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 09:54:17 +0100 Subject: [PATCH 390/818] adding easyconfigs: HPL-2.2-intel-2017.02.eb --- .../h/HPL/HPL-2.2-intel-2017.02.eb | 18 +++++++++ .../i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb | 33 ++++++++++++++++ .../iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 18 +++++++++ .../ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb | 36 ++++++++++++++++++ .../i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb | 20 ++++++++++ ...2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 38 +++++++++++++++++++ ....174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 35 +++++++++++++++++ .../easyconfigs/i/intel/intel-2017.02.eb | 24 ++++++++++++ 8 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2017.02.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb new file mode 100644 index 0000000000..976ad59fb7 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2017.02'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..cd7f8184fe --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] + +checksums = ['1ed9e5176b30ed0f0917a7ea698021ee'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..a3141d5631 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iccifort' +version = '2017.2.174' +versionsuffix = '-GCC-6.3.0-2.27' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..c4b671b697 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] + +checksums = ['9d5dfa36a36b7c9e877745f3e379248b'] + +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..b0f86b1096 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017.02' +versionsuffix = '-GCC-6.3.0-2.27' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.2.174' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..c8801dee34 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2017.02-GCC-6.3.0-2.27'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..c2e9a1817a --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2017.2.174-GCC-6.3.0-2.27'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['b6c2e62c3fb9b1558ede72ccf72cf1d6'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.02.eb b/easybuild/easyconfigs/i/intel/intel-2017.02.eb new file mode 100644 index 0000000000..941245b3e6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2017.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.2.174' +gccver = '6.3.0' +binutilsver = '2.27' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', compver, '', ('iimpi', version + gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From 6cf55b6fb7840d9db16dc9885bcef520ccd906a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 10:18:10 +0100 Subject: [PATCH 391/818] remove license_file specs in impi/imkl 2017.2.174 easyconfigs --- .../i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 2 -- .../impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index c8801dee34..62ed829038 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -16,8 +16,6 @@ checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] dontcreateinstalldir = 'True' -license_file = HOME + '/licenses/intel/license.lic' - interfaces = True postinstallcmds = [ diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index c2e9a1817a..9375fca351 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -18,8 +18,6 @@ dontcreateinstalldir = 'True' components = ['intel-mpi', 'intel-psxe', 'intel-imb'] -license_file = HOME + '/licenses/intel/license.lic' - # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 051a170864a0a07b45d308ce35ef14a1dcb31137 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 3 Mar 2017 11:00:50 +0100 Subject: [PATCH 392/818] sanity check fix --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index a81bc6e8ba..d40917cf4c 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -24,11 +24,9 @@ dependencies = [ ('matplotlib', '1.5.1', '-Python-%(pyver)s') ] -options = {'modulename': 'os'} - -#sanity_check_paths = { -# 'files': ['bin/quast.py'], -# 'dirs': [''], -#} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} moduleclass = 'bio' -- GitLab From ce387d60825aa0b2ff37fe5c1b7e1a110a0a9a7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 11:40:22 +0100 Subject: [PATCH 393/818] @boegel change too long line into tmux, fix sources libevent and added sanity_check_paths to libevent --- easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb | 13 +++++++++++-- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 3 ++- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 964ec6943d..369e68366a 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -11,9 +11,18 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'https://github.com/downloads/%(name)s/%(name)s/', - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', + 'https://downloads.sourceforge.net/project/levent/release-%(version)s-stable/', ] + sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['f3eeaed018542963b7d2416ef1135ecc'] + +sanity_check_paths = { + 'files': ["bin/event_rpcgen.py"] + + ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]] + + ['include/event2/%s' % x for x in ['buffer_compat.h', 'bufferevent.h', 'bufferevent_struct.h', 'dns_compat.h', 'dns_struct.h', 'event-config.h', 'event_struct.h', 'http.h', 'keyvalq_struct.h', 'rpc_compat.h', 'rpc_struct.h', 'tag.h', 'util.h', 'bufferevent_compat.h', 'bufferevent_ssl.h', 'buffer.h', 'dns.h', 'event_compat.h', 'event.h', 'http_compat.h', 'http_struct.h', 'listener.h', 'rpc.h', 'tag_compat.h', 'thread.h', 'visibility.h']], + 'dirs': ["lib"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index d9aa356199..d8ea21b236 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -5,7 +5,8 @@ version = '2.3' homepage = 'http://tmux.sourceforge.net/' description = """tmux is a terminal multiplexer. It lets you switch easily -between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" +between several programs in one terminal, detach them (they keep +running in the background) and reattach them to a different terminal.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'optarch': True} -- GitLab From 1ad34056480aec11dbfb1667b72b1e37fc15e4dc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 12:40:44 +0200 Subject: [PATCH 394/818] adding easyconfigs: GROMACS-2016.2-foss-2017a.eb --- .../g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb new file mode 100644 index 0000000000..5a3fc10eef --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.6.2'), +] + +moduleclass = 'bio' -- GitLab From ccda71acf21a6996fdc6d7b5ccc1aafc84614bc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 11:49:47 +0100 Subject: [PATCH 395/818] minor style fixes in NWChem 6.6 easyconfig --- ...vision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb index f693ccc152..27d258eaee 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb @@ -1,5 +1,7 @@ name = 'NWChem' version = '6.6.revision27746' +verdate = '2015-10-20' +versionsuffix = '-%s-Python-%%(pyver)s' % verdate homepage = 'http://www.nwchem-sw.org' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in @@ -13,18 +15,14 @@ toolchain = {'name': 'iomkl', 'version': '2017a'} toolchainopts = {'i8': True} source_urls = ['http://www.nwchem-sw.org/download.php?f='] -verdate = '2015-10-20' -sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] +sources = ['Nwchem-%%(version)s-src.%s.tar.bz2' % verdate] patches = [ 'NWChem_fix-date.patch', 'NWChem-%(version)s-parallelbuild.patch', ] -python = 'Python' -pyver = '2.7.12' -versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) -dependencies = [(python, pyver)] +dependencies = [('Python', '2.7.12')] # This easyconfig is using the default for armci_network (OPENIB) and # thus needs infiniband libraries. -- GitLab From 3fb14327fb696d1717d7cde894e720db5dbd2de3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:28:54 +0100 Subject: [PATCH 396/818] add eb Singularity-2.2.1-GCC-6.3.0-2.27.eb next step chown root:root /apps/all/Singularity/*/etc/singularity/singularity.conf chown root:root /apps/all/Singularity/*/libexec/singularity/sexec-suid chmod +s /apps/all/Singularity/*/libexec/singularity/sexec-suid --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..e11fd1f16c --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.2.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], + 'dirs': ['etc', '', 'libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From 68865c34f791fa80abd0ba566daed7de531c3761 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:35:36 +0100 Subject: [PATCH 397/818] move sanity_check_paths - files -> dirs ... libevents --- easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 369e68366a..41eaa5ab15 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -21,8 +21,8 @@ checksums = ['f3eeaed018542963b7d2416ef1135ecc'] sanity_check_paths = { 'files': ["bin/event_rpcgen.py"] + - ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]] + - ['include/event2/%s' % x for x in ['buffer_compat.h', 'bufferevent.h', 'bufferevent_struct.h', 'dns_compat.h', 'dns_struct.h', 'event-config.h', 'event_struct.h', 'http.h', 'keyvalq_struct.h', 'rpc_compat.h', 'rpc_struct.h', 'tag.h', 'util.h', 'bufferevent_compat.h', 'bufferevent_ssl.h', 'buffer.h', 'dns.h', 'event_compat.h', 'event.h', 'http_compat.h', 'http_struct.h', 'listener.h', 'rpc.h', 'tag_compat.h', 'thread.h', 'visibility.h']], - 'dirs': ["lib"] + ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]], + 'dirs': ["lib", "include/event2"] +} moduleclass = 'lib' -- GitLab From 2d1a8eba2da61b56a08904c302d3279ddeeb3408 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:55:21 +0100 Subject: [PATCH 398/818] remove '', --- .../s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb index e11fd1f16c..e1e43de48b 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -17,7 +17,7 @@ preconfigopts = './autogen.sh && ' sanity_check_paths = { 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], - 'dirs': ['etc', '', 'libexec/singularity'], + 'dirs': ['etc', 'libexec/singularity'], } moduleclass = 'tools' -- GitLab From 2e04f6c75933547906dadd119c731c43aa3ea456 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 14:04:49 +0200 Subject: [PATCH 399/818] adding easyconfigs: PLUMED-2.3.0-foss-2017a.eb --- .../easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb | 25 +++++++++++ .../g/Guile/Guile-1.8.8-foss-2017a.eb | 32 ++++++++++++++ .../libmatheval-1.1.11-foss-2017a.eb | 32 ++++++++++++++ .../libunistring-0.9.6-foss-2017a.eb | 24 +++++++++++ .../p/PLUMED/PLUMED-2.3.0-foss-2017a.eb | 42 +++++++++++++++++++ 5 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb new file mode 100644 index 0000000000..66df054b65 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--with-pic' + +sanity_check_paths = { + 'files': ['bin/gsl-config', 'lib/libgsl.a', 'lib/libgsl.%s' % SHLIB_EXT, + 'lib/libgslcblas.a', 'lib/libgslcblas.%s' % SHLIB_EXT], + 'dirs': ['include/gsl', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb new file mode 100644 index 0000000000..318524cbae --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.1'), + ('libunistring', '0.9.6'), + ('pkg-config', '0.29.1'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb new file mode 100644 index 0000000000..1d721e0ee3 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb new file mode 100644 index 0000000000..fdee6f5768 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.6' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb new file mode 100644 index 0000000000..1ed42c4139 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.3'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From b025dbb557c46605389c3ff16f68b965d5ec6c79 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 14:18:57 +0200 Subject: [PATCH 400/818] Forgot to add dependency, CMake 3.6.2. --- .../c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f496787852 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 5f471ba1e433fcd3a4e8aa6872b4aabd65e5621e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 14:24:00 +0100 Subject: [PATCH 401/818] fix failing tests due to use of \1 in sed expression in OrthoMCL easyconfig --- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 3f9e8e96b8..489da9288a 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -29,7 +29,7 @@ postinstallcmds = [ 'sed -i"" "s@/usr/bin/perl@$EBROOTPERL/bin/perl@g" %(installdir)s/orthomcl.pl', 'sed -i"" "s@/.*blastall@$EBROOTBLAST/bin/blastall@g" %(installdir)s/orthomcl_module.pm', 'sed -i"" "s@/.*formatdb@$EBROOTBLAST/bin/formatdb@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@/.*\(mcl.;\)@$EBROOTMCL/bin/\\1@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*/mcl@$EBROOTMCL/bin/mcl@g" %(installdir)s/orthomcl_module.pm', 'sed -i"" "s@/.*ORTHOMCL.*%(version)s/@\\$ENV{\'PWD\'}/@g" %(installdir)s/orthomcl_module.pm', ] -- GitLab From 71a84aa705659ffaee36fb39b5b0e66b2c29b855 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 14:45:45 +0100 Subject: [PATCH 402/818] adding easyconfigs: CMake-3.7.2-GCCcore-6.3.0.eb --- .../c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..29e1e466f9 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 5852aae17824c13929dbee276eda96b084bd1fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 14:58:57 +0100 Subject: [PATCH 403/818] adding easyconfigs: binutils-2.28.eb --- .../easyconfigs/b/binutils/binutils-2.28.eb | 19 +++++++++++++ easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 19 +++++++++++++ easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb | 26 ++++++++++++++++++ 4 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb new file mode 100644 index 0000000000..7681d5cc1f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -0,0 +1,19 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb new file mode 100644 index 0000000000..de26a2cd74 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -0,0 +1,19 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb new file mode 100644 index 0000000000..f186b0ad85 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. + It is mostly SVR4 compatible although it has some extensions + (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb new file mode 100644 index 0000000000..b74939ef09 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils/'] +sources = [SOURCELOWER_TAR_GZ] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 813f5d5f48f966ad2d6304f140cae7dc9d616350 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 15:29:03 +0100 Subject: [PATCH 404/818] adding easyconfigs: binutils-2.28-GCCcore-6.3.0.eb --- .../b/binutils/binutils-2.28-GCCcore-6.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..de910489db --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' -- GitLab From 033702853174a9f5f55f0dc776f6d17d269d4730 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 15:33:41 +0100 Subject: [PATCH 405/818] enable execution permissions on all Perl scripts in /bin for miRDeep2 --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 583f9a91f7..8a8e1422a7 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('randfold', '2.0.1'), # also provides SQUID ] -install_cmd = "cp -a mirdeep%s/src %%(installdir)s/bin" % altver +install_cmd = "chmod a+x mirdeep*/src/*.pl && cp -a mirdeep*/src %(installdir)s/bin" sanity_check_paths = { 'files': ['bin/make_html.pl'], -- GitLab From 4a2d28b655a93c55643153f035b98d982b1ba9f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 15:57:06 +0100 Subject: [PATCH 406/818] fix source_urls for flex, incl. help2man as build dep --- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 7 +++++-- .../easyconfigs/h/help2man/help2man-1.47.4.eb | 19 +++++++++++++++++++ 2 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index de26a2cd74..568be27f41 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -9,11 +9,14 @@ toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] dependencies = [('M4', '1.4.18')] -builddependencies = [('Bison', '3.0.4')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb new file mode 100644 index 0000000000..292de661e9 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c5582a708e0fdffca7f963810101a93be63047f4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 17:31:17 +0200 Subject: [PATCH 407/818] Updated dependency for Gromacs to CMake 3.7.2. Fixed missing parts in CMake 3.6.2 config. --- easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb index f496787852..50e2df64aa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb index 5a3fc10eef..8ad8f765c7 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -30,7 +30,7 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.6.2'), + ('CMake', '3.7.2'), ] moduleclass = 'bio' -- GitLab From ee8d9018a1381e77be204e32195d29de9268fc3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Mar 2017 11:40:34 +0100 Subject: [PATCH 408/818] complete release notes for v3.1.1 & bump version --- RELEASE_NOTES | 46 ++++++++++++++++++---------------------------- setup.py | 2 +- 2 files changed, 19 insertions(+), 29 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index aa222f795f..060a0725f1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,53 +3,43 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, +The latest version of easybuild-easyconfig provides 6,643 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.1 (March 3rd 2017) +v3.1.1 (March 6th 2017) ----------------------- bugfix release -- added example easyconfig files for 15 new software packages: +- added example easyconfig files for 16 new software packages: - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), - meshio (#4178), miRDeep2 (#4229), OOMPA (#4211), PBSuite (#4230), randfold (#4217), Smoldyn (#4110), - SpiecEasi (#4215), stress (#4180) + meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246), + Smoldyn (#4110), SpiecEasi (#4215), stress (#4180) - added additional easyconfigs for various supported software packages, including: - - ATK 2.22.0, Armadillo 7.600.2 + 7.800.0, arpack-ng 3.4.0, BLASR 2.2, Bazel 0.4.4, BioPerl 1.7.1, CFITSIO 3.41, - CGAL 4.9, CMake 3.7.2, Cantera 2.3.0, cURL 7.52.1, DMTCP 2.5.0, Eigen 3.2.10 + 3.3.2 + 3.3.3, Emacs 25.1, - ea-utils 1.04.807, freetype 2.7.1, GMP 6.1.2, Graphviz 2.38.0, gettext 0.19.8.1, IPython 5.2.2, JasPer 2.0.10, - Java 1.8.0_121, Lmod 7.3, libQGLViewer 2.6.4, libpng 1.6.27 + 1.6.28, likwid 4.2.0, MCL 02.063 + 14.137, - MCR R2013b + 2014b + R2015b + R2016b, matplotlib 2.0.0, networkx 1.1, OpenSSL 1.1.0e, OrthoMCL 1.4 + 2.0.9, - PCRE 8.40, PyTables 3.2.3.1, Pysam 0.10.0, path.py 10.1, prompt-toolkit 1.0.13, Qt5 5.8.0, ROOT 6.06.02, - SCons 2.5.1, Stacks 1.44, StringTie 1.3.3, sickle 1.33, VTK 7.1.0, ViennaRNA 2.2.3, Vim 8.0, XZ 5.2.3, - Yade 2017.01a -- added easyconfigs for new 'iomkl/2017a' and 'iompi/2017a' toolchains (#4216) + - binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0, + PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a +- added new easyconfigs for existing toolchains: + - iomkl/2017a (#4216), intel/2017.02 (#4248) - various enhancements, including: - - clean up dependencies in libdrm (#4113) - - update X11 bundle and dependencies for GCCcore-6.3.0 (#4147) - - fix style in several easyconfigs (#4174, #4176, #4190) + - fix style in several easyconfigs (#4174, #4176, #4190, #4233) + - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) + - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) - various bug fixes, including: - - allow intel 2017 to compile (#4102) - - work around build failure with GCC 6 in pkg-config (#4109) - add Bison and gettext as build deps for X11 (#4111) - - fix ippicv source download and library install in OpenCV (#4126) - - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4135) + - clean up dependencies in libdrm (#4113) + - make sure Ghostscript picks up external libraries (#4118) + - fix ippicv source download and library install for OpenCV v3.1.0 (#4126) + - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4134, #4135) - get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146) - remove duplicate sources specification in OpenMPI (#4150) - - fix definition of buildopts/installopts in Cantera easyconfig (#4164) + - fix definition of buildopts/installopts in Cantera easyconfig (#4133, #4164, #4177) - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) - - fix broken test in Cantera 2.3.0 rather than skipping it (#4177) - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) - - update $PATH in OrthoMCL 1.4 easyconfig (#4182) - - bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a (#4188) - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) - - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) - - set CMAKE_PREFIX_PATH to ncurses install directory (#4196) + - set CMAKE_PREFIX_PATH to ncurses install directory in CMake easyconfigs (#4196) - switch to lowopt=True for libxc v2.2.* and v3.* (#4199) - remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200) - fix version (& homepage) in ea-utils easyconfigs (#4205) - remove --with-threads configure option in OpenMPI-2.* (#4213) - - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) - fix check for Szip library in configure script for netCDF 4.1.3 (#4226) - fix source_urls in several easyconfigs, including: - bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227) diff --git a/setup.py b/setup.py index a3f5efb8ac..2cd1801e1b 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.1.0' +VERSION = '3.1.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 7b15ed20fa7b321bb2ef12657e381d1a1c57bc8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 6 Mar 2017 08:00:12 +0100 Subject: [PATCH 409/818] 'dummy' -> '' --- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index d8ea21b236..0423702965 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -8,7 +8,7 @@ description = """tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -- GitLab From bb62863e09d4935fe68e96b4055e023014bd2e5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 11:39:09 +0100 Subject: [PATCH 410/818] adding easyconfigs: SPAdes-3.10.1-foss-2016b.eb --- .../s/SPAdes/SPAdes-3.10.1-foss-2016b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb new file mode 100644 index 0000000000..c4ecdeaede --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.10.1' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Boost', '1.63.0', '-Python-2.7.12'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bwa-spades', 'dipspades', 'dipspades.py', + 'hammer', 'ionhammer', 'spades', 'spades.py']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 08689b0d378055ebfe07de920e6a08974761792f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 13:25:09 +0100 Subject: [PATCH 411/818] add easyconfig for missing CMake dep --- .../c/CMake/CMake-3.7.2-foss-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb new file mode 100644 index 0000000000..1d41f93b9b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ff49dc26d982489ed1ade8b1e5fd821c2dc239d6 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 6 Mar 2017 14:28:40 +0100 Subject: [PATCH 412/818] add sanity check python module --- .../r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb index 6bb0455477..902a9ecafd 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -42,6 +42,8 @@ configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' configopts += '-Dcxx14=ON ' configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' +sanity_check_commands = ["python -c 'import ROOT'"] + modextrapaths = {'PYTHONPATH': 'lib/'} moduleclass = 'data' -- GitLab From de7e657c88579abd4e19329524edce969ff8dce6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 6 Mar 2017 18:47:52 +0100 Subject: [PATCH 413/818] adding easyconfigs: awscli-1.11.56-foss-2016b-Python-2.7.12.eb --- ...awscli-1.11.56-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..729a10008f --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'awscli' +version = '1.11.56' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' -- GitLab From adfd421614f445e8fb39495272de39760de504d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 18:57:47 +0100 Subject: [PATCH 414/818] {lang}[intel/2017a] Python v2.7.13 --- .../g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb | 31 ++++ .../libreadline-7.0-GCCcore-6.3.0.eb | 33 +++++ .../p/Python/Python-2.7.13-intel-2017a.eb | 133 ++++++++++++++++++ .../p/Python/numpy-1.12.0-mkl.patch | 55 ++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb | 30 ++++ 5 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..046f2d1718 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('binutils', '2.27'), + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a64400af8e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '7.0' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +builddependencies = [('binutils', '2.27')] +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb new file mode 100644 index 0000000000..31e0d3d932 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.13' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 6th 2017 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch new file mode 100644 index 0000000000..3d09924f96 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9dca9f6e5c --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From cf160c44110226e8f37de1d8e3e235af08a0a369 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 08:55:17 +0100 Subject: [PATCH 415/818] bump easyconfig files count in release notes --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 060a0725f1..1c930d74fe 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,643 easyconfig files, for 1,168 different software packages, +The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.1.1 (March 6th 2017) -- GitLab From 36877ded32473a03edb33e9d27e99a7f498fc7e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 08:57:52 +0100 Subject: [PATCH 416/818] fix release date for EasyBuild v3.1.1 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1c930d74fe..96a76caa5a 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.1 (March 6th 2017) +v3.1.1 (March 7th 2017) ----------------------- bugfix release -- GitLab From 533a573a1c8455697a72bd8883503a86c13bf7c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 15:21:30 +0100 Subject: [PATCH 417/818] bump version to 3.2.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2cd1801e1b..0683e432c9 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.1.1' +VERSION = '3.2.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From fde809e0021a1eb648084501f5b8c547cdd255f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 16:24:48 +0100 Subject: [PATCH 418/818] adding easyconfigs: EasyBuild-3.1.1.eb --- .../e/EasyBuild/EasyBuild-3.1.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb new file mode 100644 index 0000000000..2dbc7fa9ba --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/ef/c7/640c6d791ba452321c0d1371b6626486bb495e0645bb896d33c78a09f810', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/f2/19/1c79b1ad24f0004e9507f12d4222367611f42ac479abd6315a50a23c52f5', + # easybuild-easyblocks + 'https://pypi.python.org/packages/87/aa/2a19f05c78dd2550f7bd42ef0964b9c51c5626c1e715c2ee0a4f778780b8', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/e6/68/5e977f549bf04b8cd87cdc5179d8b36c1eb971cfe3c43f98053f2dbe9c64', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.25.tar.gz', + 'vsc-base-2.5.7.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 65002095722c407e0105a5f67bb6950a788793c4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 11:08:55 +0800 Subject: [PATCH 419/818] yet another batch of minor style fixes --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb | 3 ++- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 3 ++- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb | 3 ++- .../a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb | 3 +-- easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb | 3 +-- ...-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb | 2 +- .../Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb | 2 +- ...6.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb | 5 ++++- .../easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb | 5 +++-- 23 files changed, 57 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index 094f648512..1b2933e3ca 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.12.1' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index f899ce8f01..e7d7f8108e 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.13.5' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index 2063066a88..77fcbc5c08 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.14.1' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb index bde2863301..6fb42921f6 100644 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 0e9c615ba9..70205ebf3a 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb @@ -15,7 +15,6 @@ sources = ['advisor_xe_%(version)s.tar.gz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb index 22d5bebaad..6e2edca0dc 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -17,7 +17,6 @@ checksums = ['af87b381394be3100507827a3461b3bc'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb index 4e451954c3..4e75833d6e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '16' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (5, 14) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb index f910ba5400..b2fcc5fada 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '16' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (5, 14) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index 1b29f57d52..8895c479d8 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '16' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (5, 14) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb index 3d86e53a57..552c3eb907 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb @@ -4,7 +4,10 @@ name = 'Autoconf' version = '2.69' homepage = 'http://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure + software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual + user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating + system features that the package can use, in the form of M4 macro calls.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb index 1e344106ca..612bf18994 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb @@ -4,7 +4,10 @@ name = 'Autoconf' version = '2.69' homepage = 'http://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure + software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual + user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating + system features that the package can use, in the form of M4 macro calls.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb index 69f6af4aa8..ffe0aa3aaf 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.8.4' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb index ed48c65191..f37d535fe6 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.8.4' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb index 4e4944c69e..7a79bafbc3 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.0' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb index b01a6297fc..ab777254e9 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.0' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb index ad986bd576..03ba48168e 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.3' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb index e1662e8bf2..986e3e5a6f 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.3' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb index 7da7aa32db..6036bb0be8 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.6' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb index 3ee7c5b406..d51a118fba 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb index d93ecdb14e..0e7df6fdf1 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb index b048fcd097..33aa30131b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.6' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb index 407fa7e1c0..0f10c1689b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb index 08bcaf86cf..f22f0e01b7 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} -- GitLab From 645b2a7dc2bad09463a04674595d23417da5a78c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 11:30:46 +0800 Subject: [PATCH 420/818] yet another batch of minor style fixes --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 +- .../easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb | 5 +++-- .../b/BCFtools/BCFtools-1.2-intel-2015a.eb | 3 ++- .../easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 3 ++- .../b/BCFtools/BCFtools-1.3-intel-2016a.eb | 3 ++- .../easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb | 6 +++--- easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb | 3 ++- .../b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb | 3 ++- easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb | 3 ++- .../easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 3 ++- .../b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb | 1 - .../easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb | 11 +++++------ .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 6 ++---- easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb | 2 +- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- .../BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 1 - .../Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Biopython-1.65-foss-2016a-Python-2.7.11.eb | 3 ++- .../Biopython-1.68-foss-2016b-Python-2.7.12.eb | 3 ++- .../Biopython-1.68-intel-2016b-Python-2.7.12.eb | 3 ++- .../Biopython-1.68-intel-2016b-Python-3.5.2.eb | 3 ++- .../Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb | 2 +- .../easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb | 4 ++-- .../easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb | 4 ++-- .../b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 9 +++------ .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 9 +++------ 30 files changed, 56 insertions(+), 53 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 76e04042bc..938cb4bc7e 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index d1646b7dbe..83c91ab617 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 7e9be8c9b6..52eabb1bfe 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -10,7 +10,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [('Java', '1.8.0_112', '', True)] diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 2ee4f62216..3ef62f1ae2 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb @@ -4,8 +4,9 @@ name = 'BCFtools' version = '1.2' homepage = 'http://www.htslib.org/' -description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index f9319eca14..41baab6d42 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -5,7 +5,8 @@ version = '1.2' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index 6d469bdd3b..a0b589e82c 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -5,7 +5,8 @@ version = '1.3' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb index bd1b04228a..af2dc1fef7 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb @@ -5,7 +5,8 @@ version = '1.3' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb index 47aaf73fa3..4ed43caefd 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb @@ -27,9 +27,9 @@ parallel = 1 files_to_copy = ["bin"] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", - "starchcat", "vcf2bed", "wig2bed", - "gtf2bed", "bedops", "wig2bed"]], + 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed", "sort-bed", + "starchcat", "vcf2bed", "wig2bed", + "gtf2bed", "bedops", "wig2bed"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb index afbf2938b8..eb88b061dd 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb index e2d58bafb6..0222da1546 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb index 5f6044dcec..955ee61e30 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 9cbb01f191..2dbdeeb980 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA -# Authors:: George Tsouloupas , Fotis Georgatos , Daniel Navarro +# Authors:: George Tsouloupas , Fotis Georgatos , +# Daniel Navarro # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb index 9cd875e7c6..c0802f9ddd 100644 --- a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb +++ b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb index e948c06e11..65f14b74d8 100644 --- a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb @@ -25,12 +25,11 @@ start_dir = 'sources' parallel = 1 -files_to_copy = [(['sources/g_baypass'], 'bin/'), - 'BayPass_manual_2.1.pdf', - 'examples', - 'Licence_CeCILL-B_V1-en.txt', - 'utils' -] +files_to_copy = [(['sources/g_baypass'], 'bin/'), + 'BayPass_manual_2.1.pdf', + 'examples', + 'Licence_CeCILL-B_V1-en.txt', + 'utils'] sanity_check_paths = { 'files': ['bin/g_baypass'], diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 20f57806c7..0d36886635 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -4,9 +4,7 @@ name = 'BayesAss' version = '3.0.4' homepage = 'http://www.rannala.org/?page_id=245' -description = """ -BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes -""" +description = "BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes" toolchain = {'name': 'foss', 'version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] @@ -21,7 +19,7 @@ runtest = 'check' sanity_check_paths = { 'files': ['bin/BA3'], - 'dirs' : ['bin', 'include'] + 'dirs': ['bin', 'include'] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 972161d135..283940594d 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -18,7 +18,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o toolchain = {'name': 'dummy', 'version': ''} -source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] +source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] sources = ['BEASTv%(version)s.tgz'] dependencies = [ diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 5afb842c80..ff35b3fe93 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2 installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+prog+'.'+flavor+'.x' + 'files': ['bin/' + prog + '.' + flavor + '.x' for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 9d064dae20..0f2dfc0807 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2 installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+prog+'.'+flavor+'.x' + 'files': ['bin/' + prog + '.' + flavor + '.x' for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 2661f0fe38..c32f54aa1d 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -37,4 +37,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index a3dca17749..26ff0e4f6a 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index 5efa64f0e0..462ab92f17 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index a42f248efe..c5aa94f58c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb index 1c5fd3f356..f5a410bf23 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb index 953304846e..762f84f558 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb index b22f51705c..36d03b946c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb index b906f81abf..24c748d95f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -18,7 +18,7 @@ pythonversion = '2.7.11' versionsuffix = '-Python-%s' % pythonversion dependencies = [ - ('bzip2', '1.0.6' ), + ('bzip2', '1.0.6'), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb index 95d2b2fb64..bcb89c1b4e 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb @@ -19,8 +19,8 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] - + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb index d23fa88f57..dce0112a41 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb @@ -19,8 +19,8 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] - + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index 29785ed5e6..49900e2203 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -2,12 +2,9 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' version = '2.1.2' -homepage= 'https://github.com/beagle-dev/beagle-lib' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index ba27dc855d..eb31afb551 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -3,12 +3,9 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' version = '2.1.2' -homepage= 'https://github.com/beagle-dev/beagle-lib' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From cb34f841946cc8f5be8a95031e763e7c2ddc4c9d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 14:41:26 +0800 Subject: [PATCH 421/818] yet another batch of minor style fixes --- .../easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb | 14 +++++++------- easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb | 3 ++- .../easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb | 3 ++- .../CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb | 5 +++-- .../CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 9 ++++----- .../Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 3 ++- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb | 3 ++- .../Cython-0.24.1-foss-2016a-Python-2.7.11.eb | 3 ++- 14 files changed, 37 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb index fbd1e0f85d..137bbb1603 100644 --- a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb @@ -4,13 +4,13 @@ name = 'CLooG' version = '0.18.1' homepage = 'http://www.bastoul.net/cloog/index.php' -description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. -That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. -CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. -Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best -polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user -has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code. -""" +description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a + code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been + originally written to solve the code generation problem for optimizing compilers based on the polytope model. + Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the + best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While + the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a + very effective code.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb index 299410b70c..8997152413 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb @@ -36,7 +36,8 @@ elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION else: - print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % (OS_NAME, OS_VERSION) + OS = (OS_NAME, OS_VERSION) + print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % OS system = 'ubuntu11.10' elif OS_NAME == "opensuse": system = 'suse12.1' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb index 9b2a072f8b..194a2991a9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb @@ -36,7 +36,8 @@ elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION else: - print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % (OS_NAME, OS_VERSION) + OS = (OS_NAME, OS_VERSION) + print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % OS system = 'ubuntu11.10' elif OS_NAME == "opensuse": system = 'suse12.1' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb index 071eb0169f..e06141ece5 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb @@ -5,8 +5,9 @@ version = '1.1.5' homepage = 'http://abel.ee.ucla.edu/cvxopt/' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. -Its main purpose is to make the development of software for convex optimization applications straightforward -by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.""" + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb index 3e32468f92..795f2f0360 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb @@ -5,8 +5,9 @@ version = '1.1.5' homepage = 'http://abel.ee.ucla.edu/cvxopt/' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. - Its main purpose is to make the development of software for convex optimization applications straightforward - by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.""" + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 112a9312bc..8f554a1eb2 100644 --- a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -9,11 +9,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version - ('PrgEnv-pgi', EXTERNAL_MODULE), - ('pgi/16.3.0' , EXTERNAL_MODULE), - ('cray-mpich/7.3.2', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-pgi', EXTERNAL_MODULE), + ('pgi/16.3.0', EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb index fa53744e7c..e22250c990 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.16' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb index f2fb277465..33b4c1bc5b 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.16' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb index 0e8ac631d0..ec51d696a0 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.19.1' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb index 6ba8ee3375..1cdbf2c1fc 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.19.1' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb index 80955e4cc6..8494b353e5 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -5,7 +5,8 @@ version = '0.19.2' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 1a87b1c99c..769f55ce72 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.22' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. -Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb index 426fedf887..dd9fc1ad56 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb @@ -6,7 +6,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. -Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb index a2db0bddbe..0dfcb1056b 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb @@ -6,7 +6,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. -Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From b2c06bc2d82e3c1e666cff29ade846e11e5eade3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 14:59:09 +0800 Subject: [PATCH 422/818] yet another batch of minor style fixes --- easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb | 2 +- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 1 - easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 3 ++- easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 3 ++- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 3 ++- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 3 ++- easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb | 1 - easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb | 1 - easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 2 +- 10 files changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb index fcf1bd7696..b1a5625761 100644 --- a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -15,4 +15,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 8c069fec94..03f4831ace 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'data' - diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index 7071afdb2c..c041d6e2aa 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,7 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', + 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index 0940c66fb5..e933c1af39 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -16,7 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', + 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index f322881382..74d90eb777 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -16,7 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', + 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 99e680c26d..389f7d8425 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -4,7 +4,8 @@ name = 'DFT-D3' version = '3.1.1' homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' -description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb index 597de0792e..04e4fd7a51 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb index 3f64420e2e..1687e9b44d 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index ed4f3f692d..3d7e8e50d6 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 3f01a8dfb9..33794a918d 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], -- GitLab From 7573dd7036cbb7fd602b4a4c786a4b6c924b0413 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 15:06:39 +0800 Subject: [PATCH 423/818] yet another batch of minor style fixes --- .../e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb | 12 ++++++------ .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 3 ++- .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 3 ++- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb index 6b962c6687..a429626ec5 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb @@ -11,12 +11,12 @@ name = 'EIGENSOFT' version = '6.1.1' homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) - and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components - analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; - the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, - minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in - plotting script and supports multiple file formats and quantitative phenotypes.""" +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. + 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal + components analysis to explicitly model ancestry differences between cases and controls along continuous axes of + variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral + populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT + package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 89cd537fc7..5d29ad3201 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +configopts += 'LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index bbbc8c56b4..b5d3e358e9 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +configopts += 'LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' -- GitLab From b9e4dd100da43895e59db82f464b1e4c11a84ce8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 08:43:10 +0100 Subject: [PATCH 424/818] adding easyconfigs: PGI-17.1-GCC-6.3.0-2.27.eb --- .../p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..6502b349fb --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '17.1' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['836f536ad8b0aac0234f7528fbd56b62'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From ebd527a224dce1fa117b30a94a8f5fd5ab75a0fc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 16:15:51 +0800 Subject: [PATCH 425/818] yet another batch of minor style fixes --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 2 +- easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb | 6 +++--- .../easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb | 3 ++- easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb | 3 ++- .../f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb | 3 ++- 25 files changed, 50 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb index c1501d5c82..cb997fa593 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb index 6b9a39e112..31a89c0085 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index d7d711211d..aee9c310da 100644 --- a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), ('HDF5', '1.8.16'), -# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile + # ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile ] # define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 59de3272db..1788c8a21a 100644 --- a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -9,9 +9,9 @@ name = 'Firefox' version = '44.0.2' homepage = 'https://www.mozilla.org/en-US/firefox/new/' -description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code - base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy - and security measures, smart searching, and RSS live bookmarks.""" +description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the + Mozilla code base and offers customization options and features such as its capability to block pop-up windows, + tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb index 09e345ac68..7e51dd88f4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb @@ -13,7 +13,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb index f0c8e977f8..bcf6608413 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb @@ -12,7 +12,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb index dafae024b0..916f1302f2 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb @@ -13,7 +13,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb index 93ed64ef31..26eaffc5f6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb @@ -12,7 +12,8 @@ source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb index c7a87aa9ac..cbbe1daafc 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb index 5fa7fbc89e..a5e70027fa 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb index 6af71f85ba..8fa382b0ca 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb index 7424371c29..0571a145ad 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.9')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb index 1840f18b99..cea107f292 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb index cf4ca6186c..9b0aae30b7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb index 68312d108d..45d6dc8e93 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb index e9f0fd7c95..c9b6e770b4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb index 5eb7f91b58..07f4f8160c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb index ca24a618dc..44080cb0f8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb index 8978812458..7cfa18b2f4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb index af7228f4f5..78c7fb98d6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb index 316e040e08..4cf88e23a7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb index 32b12425a8..8405a0ec93 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb @@ -16,7 +16,8 @@ versionsuffix = '-libpng-%s' % libpngver dependencies = [('libpng', libpngver)] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb index 0913227caf..9c9d2b2e08 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.18')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb index 32c4b9ab5c..bbfd2a2508 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.20')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb index 54449d2405..912f826139 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } -- GitLab From 16127fff4d6a6db5774b196d529850bdf34fc427 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 09:21:20 +0100 Subject: [PATCH 426/818] revert back to using shipped Boost for SPAdes 3.10.1, since Boost version difference is too big --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb index c4ecdeaede..6e5c9aeb32 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -20,10 +20,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://cab.spbu.ru/files/release%(version)s'] sources = [SOURCE_TAR_GZ] -builddependencies = [ - ('CMake', '3.7.2'), - ('Boost', '1.63.0', '-Python-2.7.12'), -] +builddependencies = [('CMake', '3.7.2')] dependencies = [ ('zlib', '1.2.8'), -- GitLab From fc7300777ea6b8d9938c626e0f3642a3f7e4119b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 16:45:11 +0800 Subject: [PATCH 427/818] yet another batch of minor style fixes --- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb | 3 ++- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb | 1 - .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb | 4 ++-- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb | 4 ++-- .../g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb | 4 ++-- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb | 4 ++-- .../easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb | 3 ++- .../easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb | 3 ++- easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb | 3 ++- .../g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb | 4 ++-- easybuild/easyconfigs/g/gompi/gompi-2016.07.eb | 4 ++-- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 3 ++- 27 files changed, 51 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 69dadef3c7..bae4a90d91 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index c8e83f1af6..88a772e2f8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index e60f317150..d0d5a239b6 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 47af207c6f..b6d45b10ea 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index 9faee44d8b..935f73ec90 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index fa068137af..6ed0f40863 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb index 9d0b198d0f..afc148cb14 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 4cfb618383..e5810437c4 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 70eb5b0a10..0a33e2b925 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 477760c3c0..49772e1a73 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index d952c14671..98f0d96369 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb index 73ce1be6d6..fecad61365 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index 918c5aec06..b29b2e7ddf 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb index 3e8dd8b2df..ffe44a8cda 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb index cabfe78d32..ba98f92742 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb index ab0d6b9ba8..e822e11f35 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb index 7fae7e2b3f..adf36de398 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb index 83b2732fb5..f52ab6e342 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb index 350a3d6cfa..3f046b2129 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb index f8d1e53e32..5f20cd92b4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb @@ -28,8 +28,8 @@ source_urls = [ sources = [ SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', + # seems to have disappeared? + # 'regressiontests-5.0.2.tar.gz', ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb index fa06ee75b2..dd5cd622b8 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -10,7 +10,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_subdir = 'gs%(version_major)s%(version_minor)s' +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb index 8612f2848b..59430c9acb 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -10,7 +10,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_subdir = 'gs%(version_major)s%(version_minor)s' +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb index 43c5a459fa..af08c394ee 100644 --- a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb @@ -4,7 +4,8 @@ name = 'Grep' version = '2.21' homepage = 'http://www.gnu.org/software/grep/' -description = """The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.""" +description = """The grep command searches one or more input files for lines containing a match to a specified pattern. + By default, grep prints the matching lines.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb index 991e6da6fa..fe0e24229f 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -46,4 +46,4 @@ sanity_check_paths = { modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb index bd4f6deeb9..c16d2b51eb 100755 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -25,8 +25,8 @@ sanity_check_paths = { # add the installation dir to PATH modextrapaths = { - 'PATH': '', - } + 'PATH': '', +} # remove exec permission for the provided installation script postinstallcmds = ["chmod og-x %(installdir)s/install.sh"] diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb index 5eca4152c8..eec2b277ee 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -15,8 +15,8 @@ gccbinver = '%s-%s' % (gccver, binutilsver) # compiler toolchain dependencies dependencies = [ - ('GCC', gccbinver), # includes both GCC and binutils - ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), + ('GCC', gccbinver), # includes both GCC and binutils + ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index a0f2ba3078..2f14396e13 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,7 +21,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', + 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], } -- GitLab From 068f2709b301b502210412079179f44b4f9865b5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:02:26 +0800 Subject: [PATCH 428/818] yet another style fix --- easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index c041d6e2aa..2a15cb846c 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,8 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', - 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } -- GitLab From c3c6264ef9172d1aab091bb2ba6c0bd42b16ac07 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:12:07 +0800 Subject: [PATCH 429/818] yet another style fix --- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 5d29ad3201..c9a900612f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -23,8 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -configopts += 'LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index b5d3e358e9..9783862078 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,8 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -configopts += 'LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' -- GitLab From f0ad795a7ccf37af9a466968552f3feee9e98dcb Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Wed, 8 Mar 2017 10:26:58 +0100 Subject: [PATCH 430/818] Correction: EBROOTLIGJPEGTURBO -> EBROOTLIBJPEGMINTURBO --- .../easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb index 63e63419b2..5eee841793 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb index 6355e7d5d7..6e30f9da8c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb @@ -32,7 +32,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb index 9e5b8f7b62..d2c01232d3 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb @@ -34,7 +34,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment -- GitLab From f2188cf1ad91631353221a858924aae5cbf26719 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:32:58 +0800 Subject: [PATCH 431/818] yet another style fix --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 7 ++----- easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb | 4 ++-- .../g/Ghostscript/Ghostscript-9.19-intel-2016a.eb | 2 +- .../g/Ghostscript/Ghostscript-9.19-intel-2016b.eb | 2 +- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 4 ++-- 11 files changed, 20 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index e5810437c4..a4b668c8cb 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 0a33e2b925..ec6e1d4b8c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 49772e1a73..33b05c7f1c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 98f0d96369..3d36571118 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb index fecad61365..02f569f33b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index b29b2e7ddf..08fc164519 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb index ffe44a8cda..8ed215628a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb index ba98f92742..0cfae7ee91 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb index dd5cd622b8..9a3a3ea548 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} source_subdir = 'gs%(version_major)s%(version_minor)s' -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb index 59430c9acb..0d5843bdd6 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_subdir = 'gs%(version_major)s%(version_minor)s' -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index 2f14396e13..8dc32d3aad 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,8 +21,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', - 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', + 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], } -- GitLab From 52d921264b76ac2563135e32a93f5df07a4b0be6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:37:23 +0800 Subject: [PATCH 432/818] yet another batch of minor style fixes --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 3 ++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb | 6 +++--- .../h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 6 +++--- .../h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb | 6 +++--- .../easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb | 7 ++++--- .../easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb | 7 ++++--- .../easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb | 9 +++++---- .../easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb | 7 ++++--- easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb | 2 +- .../h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 2 +- .../easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb | 7 ++++--- .../h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- 84 files changed, 245 insertions(+), 232 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index 28e5e6ad36..e115932f8e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.11' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index fa2a08d015..16556a59b7 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.8' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index b1098f85e1..7250d32fe5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -24,4 +24,4 @@ dependencies = [ ('libxml2', '2.9.3') ] -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 76836f3aed..259d3f70b6 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -16,7 +16,8 @@ name = 'HPCBIOS_Debuggers' version = '20130829' homepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-05.html' -description = """Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel codes.""" +description = """Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel + codes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb index 576cc9a699..5feb085a79 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb index cf3bd5fd41..0715af27f9 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb index d327bfbbab..cd888a1b77 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb index fa3e730343..96f1d5781a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb index 91a1cadef9..e3f05fd328 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb index 934cc8d3eb..4edf03da45 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayCCE', 'version': '2015.06'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb index 7a8e5a0800..76ee40d652 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayCCE', 'version': '2015.11'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb index 4f4dbfc813..2c9f0ea5ba 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb index 455f495e6e..bff436a5d6 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb index f64bec348b..b1fe7ccd3c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb index 57414cfc79..c7a116c4f3 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb index b59f7317b1..b9880180b4 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb index 00ee4facc9..4749294d9f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb index 651ae824ba..32ea90665e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb index 9ab9de3734..ab2e745599 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb index 6e7b16eb21..c750f970fb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb index 225cb3be6a..97e132a043 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb index 728ad9cf2e..fe7bda0c23 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb index e65fa73eda..6c486063ce 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb index e44a4ac54d..416d5bc913 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb index e43e4270dd..df93eaf60f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb index 5634e6bd4f..c40112704f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb index 50fef4fac6..5d0475520c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'usempi': True, 'openmp': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb index ae8a971cbf..7513b5c69c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gmpolf', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb index dda08f35b9..7a3660c3cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gmvolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb index d581afc6f7..b99e6ef61e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gmvolf', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb index fd109a8fed..51de797385 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb index 92f6036e1c..036b47fd97 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb index 55ab924d7d..7fd7fc7bf8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb index 38c3e337e3..595430c600 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb index 4c3646267b..095ac318fe 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.10'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb index 4e8b437981..271e44e3ae 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb index 07ff11637e..1740a95776 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb index 7597cf43f8..bfca06cd24 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015.02'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb index 4e727e3fcd..0be6dec3cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015.08'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb index 97b6ceedd3..774ed3383d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb index fa34ec665e..ecdaa77a80 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb index 406d3ae039..3f8d9be6d0 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.00'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb index 27b235374a..7fa2f28990 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.01'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb index 977c7d487d..21af879c00 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb index ffa453cdb4..d6bd01277c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb index f2d54cf671..2c8b3ccfcc 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.03-GCC-4.9'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb index 7eaca67c16..eb86100453 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb index 660c68898c..3aa6c8de88 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.4'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb index a3af786ca9..2349780aef 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb index 226f45477c..f4cc398833 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb index e2c8df3cc6..8cc92060d3 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2015.01'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb index 28511646d6..645f1e333c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2015.02'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb index 59e1705669..2247657f83 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2015.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb index 42249afb29..ac09c4d824 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb index 9552b4d653..2f6f29630a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb index 4d48990b54..9b006fcd88 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb index 112d6aa634..23e9cfc7a8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.09'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb index c44018425b..09db015192 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb index be4db4593e..0766c10887 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.09'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb index e59ac471b9..95e36ebf95 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb index d1430d0e3a..c13e143bbf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolfc', 'version': '2016.08'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb index fff961832d..069cc730f1 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolfc', 'version': '2016.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb index 48447ddb28..d09d150a57 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017.00'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb index 64700f3b27..0db9bffabb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017.01'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb index 976ad59fb7..f53793fe5b 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017.02'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb index 80e701d1a6..6caac90930 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb index 05f316bde4..b6258c055e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intelcuda', 'version': '2016.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index 22cd32989a..579a293142 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb index efda5a282c..ed855cdf2a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-5.4.0-2.26'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb index d890354a7b..37c0a37f5d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2017.01'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb index 77dc4ed21f..77467edaf2 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb index 005a57564c..3ef2663a61 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.09'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb index d46bdf7367..3b8e366300 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.3.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given -a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) -in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb index 44e47d185b..c2eb89d992 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.3.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb index 783b534519..f62ed07a47 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.4' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} @@ -16,4 +17,4 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb index 8b0afc7b1f..cf92cc3c69 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.4' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb index 80e0503ba7..5ab80c6f39 100644 --- a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'Hoard' version = '3.10' homepage = 'http://www.hoard.org/' -description = """Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications.""" +description = "Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 17626346c5..1807b63953 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'h5py' version = '2.0.1' homepage = 'http://code.google.com/p/h5py/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. - HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of + enormous amounts of data.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index 12d6705dfa..d7449726a8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (2 * (pythonshortver, ))], 'dirs': [], } diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb index 09424f6b1b..b789858736 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb @@ -4,9 +4,10 @@ name = 'h5utils' version = '1.12.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/H5utils' -description = """h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable - HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to - convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).""" +description = """h5utils is a set of utilities for visualization and conversion of scientific data in the free, + portable HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes + programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, + Vis5d, and VTK).""" source_urls = ['http://ab-initio.mit.edu/h5utils/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 944bc27a5e..4ab8e8fc9a 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 778a209cab..401ada28ea 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb index 3f0df333bf..067d4ce450 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb index d1f6974e2a..786bdb4f54 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], -- GitLab From 8dba00cbe75ceb7740ef6134c488fba62efc5b7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:45:35 +0800 Subject: [PATCH 433/818] yet another style fix --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index a4b668c8cb..8e387e8194 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index ec6e1d4b8c..3a8e68733e 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 33b05c7f1c..b9b142b82c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 3d36571118..12435392e5 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] -- GitLab From e67ec58c9ff764e522fd00ff67a5fcecfb2ca8e9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:51:04 +0800 Subject: [PATCH 434/818] yet another style fix --- easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index e933c1af39..7dab289eff 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -16,8 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', - 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index 74d90eb777..e221d7bbc5 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -16,8 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', - 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } -- GitLab From 64e7a3722e4418e57d89348f065681af55ab9f9b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 Mar 2017 11:00:24 +0100 Subject: [PATCH 435/818] fix to be sure the HDF5 provided by easybuild is used --- easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 7b47764f47..1461dc4f22 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -23,6 +23,9 @@ dependencies = [('HDF5', '1.8.11')] skipsteps = ['configure'] +prebuildopts = 'export HDF5LIBDIR=$EBROOTHDF5/lib &&' +prebuildopts += 'export HDF5INCLUDEDIR=$EBROOTHDF5/include &&' + # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 buildopts = ' STATIC= ' diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb index ea4423904f..d31c4ec289 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -23,6 +23,9 @@ dependencies = [('HDF5', '1.8.18')] skipsteps = ['configure'] +prebuildopts = 'export HDF5LIBDIR=$EBROOTHDF5/lib &&' +prebuildopts += 'export HDF5INCLUDEDIR=$EBROOTHDF5/include &&' + # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 buildopts = ' STATIC= ' -- GitLab From 515b3bd20aba2f214e9f33d37475e64c53b907ef Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 18:24:06 +0800 Subject: [PATCH 436/818] yet another style fix --- .../h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 1807b63953..72344ad38b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ @@ -27,7 +26,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index d7449726a8..56c251d6fa 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s-serial' % (python, pythonver) prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' @@ -29,8 +28,8 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (2 * (pythonshortver, ))], - 'dirs': [], + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' -- GitLab From 2968917cdbfbd864ae1b92aed11f2321f3e049b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 18:26:07 +0800 Subject: [PATCH 437/818] yet another batch of minor style fixes --- .../easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb | 2 +- .../easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb | 2 +- .../easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb | 11 +++++------ .../IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 6 +++--- easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb | 2 +- .../easyconfigs/i/Inspector/Inspector-2013_update6.eb | 3 ++- .../Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 4 +++- .../Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb | 2 +- .../i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-11.1.075.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.10.319.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.13.367.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.3.174.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.2.146.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.3.163.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.4.183.eb | 3 +-- .../easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.0.090.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.1.133.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb | 3 +-- .../i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 3 +-- .../i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- .../i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 3 +-- .../i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/iccifort/iccifort-2015.0.090.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2015.1.133.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2015.3.187.eb | 3 ++- .../i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2016.0.109.eb | 3 ++- .../i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 3 ++- .../i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 3 ++- .../i/iccifortcuda/iccifortcuda-2016.10.eb | 3 ++- .../easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 3 ++- easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb | 3 +-- .../i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb | 3 +-- .../i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- .../i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 3 +-- .../i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb | 6 +++--- easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb | 3 ++- easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 3 ++- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb | 3 +-- .../i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb | 7 +++---- .../i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-iompi-2015.01.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb | 3 +-- .../i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb | 3 +-- .../i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb | 3 +-- .../i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb | 3 +-- .../i/imkl/imkl-11.2.2.164-iompi-2015.02.eb | 3 +-- .../i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb | 3 +-- .../imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 3 +-- .../i/imkl/imkl-11.2.3.187-iompi-2015.03.eb | 7 +++---- .../imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 3 +-- .../impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 3 +-- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 3 +-- .../impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 3 +-- .../impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 3 +-- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 3 +-- .../impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 3 +-- .../impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 3 +-- ...pi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- .../i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 3 +-- .../i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 3 +-- ...pi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- ...pi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- ...pi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/intel/intel-2014.06.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014.10.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014.11.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015.02.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015.08.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015a.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016.00.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016.01.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016a.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.00.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.01.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.02.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017a.eb | 3 ++- .../intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb | 2 +- .../intltool-0.51.0-intel-2016a-Perl-5.20.3.eb | 2 +- .../easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb | 3 ++- .../i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 ++- .../i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 3 ++- .../i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb | 1 - .../i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb | 1 - easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb | 3 +-- 210 files changed, 286 insertions(+), 363 deletions(-) diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb index 54799f31a3..bfcfa298dc 100644 --- a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name ='IMa2p' +name = 'IMa2p' version = '20151123' commit = '66e7ac7bc5e4c5bbadbd7de943465afeb4641770' diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb index 28cdb8a360..6621f7655d 100644 --- a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name ='IMa2p' +name = 'IMa2p' version = '20160804' commit = '1ebe5777ed96b878cc81109bede84dc3f7bb5e3b' diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 9e03233c20..6af67462a3 100644 --- a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -4,10 +4,8 @@ name = 'IOzone' version = '3.434' homepage = 'http://www.iozone.org/' -description = """ -IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported - to many machines and runs under many operating systems. -""" +description = """IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file + operations. Iozone has been ported to many machines and runs under many operating systems.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -22,8 +20,9 @@ files_to_copy = [ (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'report.pl', 'Changes.txt']], 'share/doc'), (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'Generate_Graphs', 'gnu3d.dem']], 'share'), (['docs/iozone.1'], 'share/man/man1'), - (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', 'Run_rules.doc']], - 'share/doc'), + (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', + 'Run_rules.doc']], + 'share/doc'), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index bc8f42751d..89001fc17a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '10.1', versionsuffix), ('prompt-toolkit', '1.0.13', versionsuffix), ] @@ -113,9 +113,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '5.1.1', { + # ('nbconvert', '5.1.1', { # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - #}), + # }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index a303238f9b..6e5acb74b1 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.14' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb index e711a7699f..00012d332d 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb index 5ae9fcabbc..a5f0f5cc5f 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb index bd7c2f7f2a..6fbb191c8b 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb index 6b38a91f39..e6211fab28 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.16' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb index a7b67d3ddf..23ff5b76f6 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.17' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 59aa3e7414..ab3458b6cb 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -2,7 +2,8 @@ name = 'Inspector' version = '2013_update6' homepage = 'http://software.intel.com/en-us/intel-inspector-xe' -description = "Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications" +description = """Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and + parallel applications""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 6966353326..5ec986a817 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,9 @@ version = '1.0.0' homepage = 'https://launchpad.net/instant' description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. -It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://fenicsproject.org).""" + It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project + (http://fenicsproject.org).""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} majorversion = "%s.x" % ".".join(version.split('.')[:-1]) diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb index 4e88df4047..06af631540 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'Instant' version = '1.0.0' homepage = 'https://launchpad.net/instant' -description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. - It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://fenicsproject.org).""" +description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. + It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project + (http://fenicsproject.org).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb index a0ac2c0885..6b3017a194 100644 --- a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name ='i-PI' +name = 'i-PI' version = '1.0-20160213' commit = '2a09a6d' versionsuffix = '-Python-%(pyver)s' diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index efeb188af2..e0c5f7e40e 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} exts_defaultclass = 'PythonPackage' exts_list = [ - # airspeed requires this specific version of cachetools + # airspeed requires this specific version of cachetools ('cachetools', '0.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], }), diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb index 25d906e87f..6db65c8a2e 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb @@ -15,8 +15,7 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb index 270e177a0c..426c8d4726 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb index 005adc34f3..367d02cc42 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb index e8019bf5f8..df976c997d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb index 17d0cd2bbe..0e9f729010 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb index cf51e4e41b..69a166ec56 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb index 4079daa6ca..5c240e5c11 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb index 818ade63f2..f259138a7e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb index 086b7132e2..c135115579 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb index 08d3496656..b9b8d9d6de 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb index 8c5cfaeab5..db58351c1b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb index 446396ee03..a1fab236a7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb index 3be64f6a79..e42dd9678e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb index be5072e46d..ace7d02238 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb index 2e5244fe91..b62448cecd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb index b742c2c7e4..939c072363 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb index e4c5184bc0..3ebed03a03 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb index 5850a5593b..26892de20b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb @@ -15,5 +15,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb index d02dca7d22..e290c96aa6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb index dba6123fdb..352973960c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb index 368b594177..13ebafc260 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb index 08a6748331..326875c307 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 8439c044f4..dbb4b84039 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index 37331a1488..ae1d56e8a6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,7 +17,6 @@ dependencies = [(gnu, gnuver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb index 55dec91be5..833da3c0c7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb index 1ca6568cb7..b9a332e3a0 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 32978c0fbe..f15a97cd30 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -29,7 +29,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index e56edba4db..18895dbe61 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -20,7 +20,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 9d56289dfc..d375c69cbb 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -29,7 +29,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb index 51b0376b09..ebdf9f10ca 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb index cb21cd2b6c..06b3d4cc94 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb index 8387432380..7029a01c14 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb index f1a5e6d54b..d51e11b541 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.0.109' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb index a66481f29c..f03bb37944 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb @@ -5,7 +5,8 @@ name = 'iccifort' version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 618d381f6e..8bf45db5e6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.1.150' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 871fae395a..7fc5fd1e8f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.2.181' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb index e07e4371a2..0b2036c9e0 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.2.181' versionsuffix = '-GCC-5.3.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 73f4eda01f..f961d74a1f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb index a1f40c75ae..f89991b41e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-5.3.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 944d7a23b2..52e91145c6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 3ed3f947b9..e2ed764a7b 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2017.0.098' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 8034a2a1e1..6e347be3a2 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2017.1.132' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 11f7aab8ea..ea60f74334 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,8 @@ version = '2017.1.132' versionsuffix = '-GCC-6.3.0-2.27' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb index a3141d5631..d622580adc 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,8 @@ version = '2017.2.174' versionsuffix = '-GCC-6.3.0-2.27' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb index 1eeb749c6e..2e8347c1be 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb @@ -4,7 +4,8 @@ name = 'iccifortcuda' version = '2016.10' homepage = '(none)' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL, with CUDA toolkit""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb index ed01c4e744..ecd5b0b755 100644 --- a/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb +++ b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb @@ -4,8 +4,8 @@ name = 'icmake' version = '7.23.02' homepage = 'http://icmake.sourceforge.net/' -description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to - provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" +description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written + to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} @@ -18,8 +18,8 @@ install_cmd += './icm_bootstrap %(installdir)s && ./icm_install strip all /' sanity_check_paths = { 'files': [ - 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', - 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' + 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', + 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' ], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb index fc33afb1ef..7f60c5dadb 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.2.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb index a6b070f713..0cd535b843 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.3.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb index aeb15217ff..feae6d3047 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.4.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb index 55b4f558df..7d3a7fe132 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.5.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb index e5194b8648..72271c8f07 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '6.1.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb index 41d6ceb53e..fca7778a45 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '6.2.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb index b3dda3d539..d54f7d5724 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '7.1.2' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb index 6190ed2906..e482585790 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '7.3.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb index c4b7144887..640705e6d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb @@ -15,8 +15,7 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb index da0e19e8a7..ee69dc8e33 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb index f8534d1717..1372125c7c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb index c0ab005da2..222eeaca4e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb index 8d6eeaafb4..ef3f60866f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb index 65ff75aa5c..5b08216822 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb index 0749ed0e0c..ad4923d074 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb index 99bf3863c6..43b7969dc4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb index 54b49ddcaf..018ac9b87d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb index 4efd890d23..d84bb054d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb index 05c638d451..e1ae8632f1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb index 901fc019cc..0b6f0c22ab 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb index 32705da10f..7b9de4dea5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb index dc69a4da5e..6402e2f9ac 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb index 8d50c3c460..c762cdb26a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb index 058b29e416..f987a0ac44 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb index 6a206056e1..a605451b28 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb index 4e061aba7c..104d8f2770 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb @@ -15,5 +15,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb index a94df9884b..420984ed94 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb index 62bde3a68e..b312c804d8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb index 419e0257c0..a775af60a0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb index 02137b7498..c2c4c3e7d1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 5767d1400f..6478030728 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index 0f54df3a82..4a9762b2d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,7 +17,6 @@ dependencies = [(gnu, gnuver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb index 8253a3390b..6e0324f9b5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb index 2fd9b5a946..446656fb7a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index 9599d68348..a32fd8278a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -32,7 +32,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 657a607db3..b40428eab7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -23,7 +23,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index 9afeb8bcc9..fdfcf853b6 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -32,7 +32,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index ddf779e0e0..b0f9d10dbb 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -17,9 +17,9 @@ source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] builddependencies = [('Autotools', '20150215')] patches = [ - 'igraph-%(version)s-no-lapack-no-blas.patch', - 'igraph-%(version)s-fix-aclocal-version.patch' - ] + 'igraph-%(version)s-no-lapack-no-blas.patch', + 'igraph-%(version)s-fix-aclocal-version.patch' +] # link against MKL rather than blas/lapack preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb index d62bc1e82f..8ea51a816a 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb @@ -4,7 +4,8 @@ name = 'iimpi' version = '7.1.2' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb index b0fe67cb26..7f36db9539 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -4,7 +4,8 @@ name = 'iimpi' version = '7.3.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 39b3d7cf7b..f12c8b0a4a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -29,7 +29,6 @@ interfaces = True m32 = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index b1eb6ee6e3..16e7150410 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -24,7 +24,6 @@ dependencies = [ interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index 91c64cfa0d..c3482af83f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -24,7 +24,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index b8769ef805..b9464f9703 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb index b5b58cc188..23c4595c45 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb @@ -23,7 +23,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb index 8adf971a63..11b669be47 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb index c1e7124884..cf9de7a5fc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb index ccd95b2a7a..beeabe2d96 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb index 74e9065d7c..36091633a7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb index 8b97b3ff26..cfa4fa1e11 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb index 471f7e9aa6..ce891766f7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb index 98e5ffd25f..d8ef766bc1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb index e04b151136..5c4db1885b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb index 0d09ac1d4b..dbddd3cc86 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb index 0fe1b14e46..66e98d5997 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index 7b7f159547..3c52f96be0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb index e37a375b7a..5ffe362a58 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index cc9f1d89b5..581df89fa9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb index 3b9cb14613..1381ccc44e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb @@ -27,7 +27,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb index 4843fd2442..b0b43aa3b0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb @@ -26,7 +26,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb index 3ad520461a..7a0a1e5352 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -3,8 +3,8 @@ version = '11.1.2.144' homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines -for science, engineering, and financial applications that require maximum performance. Core math functions include -BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + for science, engineering, and financial applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" toolchain = {'name': 'dummy', 'version': ''} @@ -29,7 +29,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb index 2114374474..846edaec6c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb index 8854a89598..82e9db5fed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb index 2559891bcc..6bbcefb5d7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 47e59ba9fc..ddbbf90fd9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb index bd599cfe0d..4b1c8e4141 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb index dcb2085bf3..7028d56135 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb index 3ce046efac..c0c59f1570 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb index a249ac518b..2ee043da29 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb index aadf66c552..490c88a422 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb index 82eec3eecb..e1fa90b6ca 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb index ccc021a957..4573f18614 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb index b76de536ee..8c6606cc65 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb index 807b5f2004..1b7dda307a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb index 0772c5ff65..5af833e7d6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb @@ -3,8 +3,8 @@ version = '11.2.3.187' homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines -for science, engineering, and financial applications that require maximum performance. Core math functions include -BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + for science, engineering, and financial applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" toolchain = {'name': 'iompi', 'version': '2015.03'} @@ -13,7 +13,6 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index f295b50925..a928de1ca4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -17,8 +17,7 @@ checksums = ['47567e38801efe273b36b5250c759af7'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index e40fb8448a..49c3e5d75b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -17,8 +17,7 @@ checksums = ['b57ff502b5f97f2f783e4bbda7ce42b3'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb index 53b6037e3f..a1225d2d74 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb index de96c38b15..c807d796b6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 6a204cb330..f95dd72e44 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 4c78a146fe..028fa649be 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -14,8 +14,7 @@ sources = ['l_mpi_pu_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index c44ccfe556..e460a1a60c 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_pu_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 001ee2403f..7828e8ee3d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -15,8 +15,7 @@ patches = ['impi_4.x_productsdb.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 6178aa2f65..209842e727 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 99cabee972..c4e43d9fa9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index c4adbe0ae3..9b5a71ce36 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 2121a1a6d9..36a86386a0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 92c9a61b43..3f28cb9676 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 3cd6a18055..ee1796488d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 22f0699649..97573c0075 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 922aa79344..5524846083 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index b7639d24d1..5301684735 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 21ed19633f..3eef4c39b6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index da5a2ab9be..de266ab029 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 9e61812d8f..81b707143d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index 9a3879ee53..91e7ec80d3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 5e4968df60..3b51024f12 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 43cd007ba4..7b345a78e7 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 28ece27457..154d705ccf 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 6f2bcda1cb..952a3f2313 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index a9d198b99f..62a9caf2ee 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 25f7950bae..46722880e7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index df72fa53c0..452ab3ddd5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 4b32c5dbb2..7de5ce16aa 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index c247bd8cc6..51baff5e35 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index 362bb90b08..51936e972d 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -14,8 +14,7 @@ sources = ['l_mpi_p_5.1.0.038.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index aafd77aff0..8d146fd342 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -16,7 +16,6 @@ checksums = ['aa4aaec41526aa5b244e531811877b01'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb index 9e343efe2e..af79fd7190 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index da4a993780..6042d117f6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -16,8 +16,7 @@ checksums = ['ec4db8f718c34f09fccf9d1c89454f0a'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/intel/intel-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb index 57c2903c57..37318d6737 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.06.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.06' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014.10.eb b/easybuild/easyconfigs/i/intel/intel-2014.10.eb index d89452f540..42ecc0b6a8 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.10.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.10.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.10' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014.11.eb b/easybuild/easyconfigs/i/intel/intel-2014.11.eb index 1bdbdfe846..82213850c0 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.11.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.11.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.11' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014b.eb b/easybuild/easyconfigs/i/intel/intel-2014b.eb index 9d433db3c4..2cc20c2772 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015.02.eb b/easybuild/easyconfigs/i/intel/intel-2015.02.eb index ab8507944b..a5c22d20a4 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.02.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015.08.eb b/easybuild/easyconfigs/i/intel/intel-2015.08.eb index f154fb6c65..fc731e26ee 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.08.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.08.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015.08' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015a.eb b/easybuild/easyconfigs/i/intel/intel-2015a.eb index 2cb7f99ce4..702e767c23 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb index e0b4b71ab1..dcc37ce659 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index 241463337a..2f03a7cc46 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -5,7 +5,8 @@ name = 'intel' version = '2016.00' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 37f96fa014..7c51ee2938 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -5,7 +5,8 @@ name = 'intel' version = '2016.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb index 41552f25a9..535ba2e732 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -6,7 +6,8 @@ gcc_maj_min = '4.9' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index 4d1e0dddac..904f548c97 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.3' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb index aa6be8f54d..c7bc45badd 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb @@ -6,7 +6,8 @@ gcc_maj_min = '4.9' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb index 3de185ca63..04c3682224 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.3' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb index 1de4297cce..fd9c783f53 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.4' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016a.eb b/easybuild/easyconfigs/i/intel/intel-2016a.eb index c858c20f53..5b6fecfd23 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2016a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016b.eb b/easybuild/easyconfigs/i/intel/intel-2016b.eb index 92aacd886c..5866da643e 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2016b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.00.eb b/easybuild/easyconfigs/i/intel/intel-2017.00.eb index ad8be63148..a3c48fa4ca 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.00.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.00' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.01.eb b/easybuild/easyconfigs/i/intel/intel-2017.01.eb index 9993bc8e47..10392160f1 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.01.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.02.eb b/easybuild/easyconfigs/i/intel/intel-2017.02.eb index 941245b3e6..e39d8da948 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017a.eb b/easybuild/easyconfigs/i/intel/intel-2017a.eb index 4e98f5a7f2..f1760e4271 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb index 0acb163cda..4d7b443901 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'GCCcore', 'version': '4.9.3'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb index 8fd4cb48f8..4d3f41da10 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb index 9d67e52066..74d4ba917e 100644 --- a/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb +++ b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb @@ -4,10 +4,10 @@ name = 'io_lib' version = '1.14.8' homepage = 'http://sourceforge.net/projects/staden/files/io_lib/' -description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment - File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded - into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. -""" +description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and + Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure + with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS + Windows.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb index aa85e82a98..a9a545eec7 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb index 544ad6da2e..e17fa43dd2 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb index f9059cff3e..93dbfc98f8 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.03' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb index 54ed73649a..5d1d743242 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.07' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb index cf9954cf88..ced0e87585 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.09-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb index 6b0377e8e3..f0219ff350 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.09-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb index 6039ebaad3..9d9e8846e6 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2017.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb index 032f6eb6a2..4d75373f4f 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb index 3c9854b3e1..9580ff5296 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb index 6ab1a7b7d5..db8c7fb2af 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index 1497f12bc7..af01ee3ccc 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -18,5 +18,4 @@ moduleclass = 'perf' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index dce7087021..2df68edb57 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -14,7 +14,6 @@ sources = ['l_ipp_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index c5381d564c..c7f19f61c1 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -14,7 +14,6 @@ sources = ['l_ipp_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index b8febc89fc..5e7c707582 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi4' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index 67482320a6..546ec40361 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi4' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index 42551d67c6..8922806632 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi5' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' -- GitLab From 30861069b7bb9df66f8c347f7ec1010ddcbbf8fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 14:26:59 +0100 Subject: [PATCH 438/818] adding easyconfigs: fqtrim-0.9.4-intel-2016b.eb --- .../f/fqtrim/fqtrim-0.9.4-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb new file mode 100644 index 0000000000..f57e94703f --- /dev/null +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'fqtrim' +version = '0.9.4' + +homepage = 'http://ccb.jhu.edu/software/fqtrim/' +description = """fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, + terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing + machines.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] +sources = [SOURCE_TAR_GZ] + +buildopts = 'release CC="$CXX" LINKER="$CXX" LDFLAGS="$LDFLAGS $CXXFLAGS"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ff7cd40c2f0a8da36dee04fb0661c1a3deb211b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:17:27 +0100 Subject: [PATCH 439/818] no need to include $CXXFLAGS into LDFLAGS, thanks @wpoely86 --- easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb index f57e94703f..4e2183f308 100644 --- a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] sources = [SOURCE_TAR_GZ] -buildopts = 'release CC="$CXX" LINKER="$CXX" LDFLAGS="$LDFLAGS $CXXFLAGS"' +buildopts = 'release CC="$CXX" LINKER="$CXX"' files_to_copy = [(['fqtrim'], 'bin')] -- GitLab From 2fa39e0e47203bebce534d5f36f30a5298d5e0f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:18:18 +0100 Subject: [PATCH 440/818] adding easyconfigs: DBG2OLC-20170208-intel-2016b.eb --- .../d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb new file mode 100644 index 0000000000..0f90c41b2a --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a3c162e9306d788f99d59fd3cfe93c4fee0a4929 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:40:56 +0100 Subject: [PATCH 441/818] adding easyconfigs: L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb --- ...folder-20141124-intel-2016b-Perl-5.24.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..dd21d5b9af --- /dev/null +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'L_RNA_scaffolder' +version = '20141124' +versionsuffix = '-Perl-5.24.0' + +homepage = 'http://www.fishbrowser.org/software/L_RNA_scaffolder/' +description = "L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.fishbrowser.org/software/L_RNA_scaffolder/downloads/'] +sources = ['L_RNA_scaffolder.tar.gz'] +checksums = ['3cc401886c452b1000d434dea776970e'] + +dependencies = [('BioPerl', '1.7.1', versionsuffix)] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', + 'delete_block', 'delete_linker', 'delete_same_fragment', 'exon_length', 'filter_scaffold.pl', + 'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block', 'form_initial_path.pl', + 'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block', + 'order', 'overlap', 'route.pl', 'search_guider', 'select', 'select_nodes'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d789421eeaf1847ca641fdd45ae509c85c2a4b82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:49:35 +0100 Subject: [PATCH 442/818] also include $LDFLAGS in compilation command --- easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb index 0f90c41b2a..82d644aaff 100644 --- a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] sources = ['%s.tar.gz' % commit] -cmds_map = [('.*', "$CXX $CXXFLAGS -o DBG2OLC *.cpp")] +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] files_to_copy = [(['DBG2OLC'], 'bin')] -- GitLab From a9d2e2ae16a0f109e81838f40bc98e395798b2a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 16:02:14 +0100 Subject: [PATCH 443/818] adding easyconfigs: BLAT-3.5-intel-2016b.eb --- .../b/BLAT/BLAT-3.5-intel-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb new file mode 100644 index 0000000000..48a47daaa1 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' +description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://users.soe.ucsc.edu/~kent/src'] + +dependencies = [('libpng', '1.6.23')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 2f20fd4e1aa1e702281a703d7bc114752e1d9b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 18:07:11 +0100 Subject: [PATCH 444/818] adding easyconfigs: STAR-2.5.2b-intel-2016b.eb --- .../s/STAR/STAR-2.5.2b-intel-2016b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb new file mode 100644 index 0000000000..05c3e56c2f --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.2b' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ["bin/STAR", "bin/STARlong"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 1dbcd246623116c0cde17cb04e85f87b6cba548d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:07:23 +0800 Subject: [PATCH 445/818] yet another batch of minor style fixes --- .../j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 2 +- .../jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 07eff74434..4dba96087d 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -10,7 +10,7 @@ version = '2.1.10r20160303' versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index ecf1089f64..37a4b9dd9a 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -9,7 +9,7 @@ name = 'jModelTest' version = '2.1.9r20160115' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 86c6bb0e2a0d992ba77efcc6a0577127d18a7b11 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:25:41 +0800 Subject: [PATCH 446/818] yet another batch of minor style fixes --- easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb | 4 ++-- .../easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb | 8 +++----- .../easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 3 ++- .../l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb | 2 +- .../l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb | 2 +- .../easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb | 2 +- .../l/libreadline/libreadline-6.2-goolf-1.7.20.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-5.4.0.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb | 8 ++++---- .../easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb | 5 +++-- .../l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-foss-2015b.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-foss-2016a.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-intel-2015b.eb | 8 ++++---- 22 files changed, 58 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb index 4228c8e824..59f694676c 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb @@ -29,8 +29,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb index c5eee2ec3d..daaaa15ecd 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb @@ -4,10 +4,8 @@ name = 'LevelDB' version = '1.18' homepage = 'https://github.com/google/leveldb' -description = """ -LevelDB is a fast key-value storage library written at Google that provides an -ordered mapping from string keys to string values. -""" +description = """LevelDB is a fast key-value storage library written at Google that provides an + ordered mapping from string keys to string values.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -19,7 +17,7 @@ files_to_copy = [ (['include/leveldb/*.h'], 'include/leveldb') ] -postinstallcmds=[ +postinstallcmds = [ 'cd %(installdir)s/lib; ln -s libleveldb.so.%(version)s libleveldb.so.%(version_major)s', 'cd %%(installdir)s/lib; ln -s libleveldb.so.%%(version)s libleveldb.%s' % SHLIB_EXT, ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb index 56cf148c48..593afa9ec4 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -16,7 +16,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb index 08a7cf496f..928179dc39 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb @@ -20,7 +20,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index accf89b9e8..785074f0f9 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -20,7 +20,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb index 8b0e336093..b4b7228f14 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb index 0f71868663..bc42f60686 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 68589245d1..0e45004907 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 60cd626d31..2316d70175 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb index ea33d4f180..e34d4affc3 100644 --- a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/xf86vmode.h']+ + 'files': ['include/X11/extensions/xf86vmode.h'] + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb index 873ae3da80..1fb8f730cc 100644 --- a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/xf86vmode.h']+ + 'files': ['include/X11/extensions/xf86vmode.h'] + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb index b76c98f402..7caa32f2db 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb @@ -19,7 +19,7 @@ configopts = "--with-pic" majminver = ''.join(version.split('.')[:2]) sanity_check_paths = { 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', - 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb index be707f2f9d..6d2b145e5d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 12e011a8ed..ade9c01fee 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 1710b5c8bc..8708402541 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index a4fb8619cb..7bfc1d634c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb index c434630db4..33e6e24615 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '6.0')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb index d7907d8655..ca93b0d47a 100644 --- a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb @@ -2,8 +2,9 @@ name = 'libsmm' version = '20111205' homepage = 'http://cp2k.berlios.de/index.html' -description = """libsmm is part of CP2K. It is a library tuned for small size matrix multiplication, - an area where regular BLAS is not so well-tuned. The source can be found in the tools/build_libssm directory of CP2K code.""" +description = """libsmm is part of CP2K. It is a library tuned for small size matrix multiplication, an area where + regular BLAS is not so well-tuned. The source can be found in the tools/build_libssm directory of CP2K code.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['CP2K-%s.tar.gz' % version] diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb index 6d7bea7d3d..5c7a628aaf 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb index 3c6b226b5a..57b9a33b63 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb index 052063704a..25d25c5148 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb index 19e0b26c92..bf35428b39 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb @@ -17,10 +17,10 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' -- GitLab From 204a49a722c80e724b395046c744d92ea1076f6b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:27:35 +0800 Subject: [PATCH 447/818] yet another batch of minor style fixes --- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 3 ++- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb | 3 ++- easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb | 7 +++---- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 7 ++++--- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 4 ++-- .../m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb | 9 +++------ .../easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb | 1 - .../m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb | 6 ++++-- .../easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 4 ++-- .../m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb | 2 +- .../m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb | 2 +- .../m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb | 2 +- .../m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb | 2 +- .../m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb | 8 ++++---- .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 2 +- .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 2 +- 22 files changed, 39 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index f289c8d654..c29dfc7a1a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -2,7 +2,8 @@ name = 'MVAPICH2' version = '1.8.1' homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' -description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. It is based on MPICH2 and MVICH." +description = """This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. + It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb index 372dd0b722..777e5a69e1 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb @@ -2,7 +2,8 @@ name = 'MVAPICH2' version = '1.9a2' homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' -description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. It is based on MPICH2 and MVICH." +description = """This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. + It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index b78da99d83..8357cd6199 100644 --- a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -8,16 +8,15 @@ name = 'Maq' version = '0.7.0' homepage = 'http://maq.sourceforge.net/maq-man.shtml' -description = """ Maq is a software that builds mapping -assemblies from short reads generated by the -next-generation sequencing machines. """ +description = """Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing + machines.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://sourceforge.net/projects/maq/files/maq/%(version)s/'] sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] -checksums= ["65edff1529c84783d0a4b9208a91efa9"] +checksums = ["65edff1529c84783d0a4b9208a91efa9"] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 57483e1d4f..ea99e518c2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '7.11.2' homepage = 'http://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - -a system for rendering interactive 3D graphics.""" + a system for rendering interactive 3D graphics.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} @@ -37,8 +38,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index ac83c1243a..55c990890f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -39,8 +39,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 810e10d3bb..4b5ad07db8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -39,8 +39,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb index 04f7962ec3..8c234a753f 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb @@ -4,11 +4,8 @@ name = 'Metal' version = '2011-03-25' homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' -description = """ -Metal - Meta Analysis Helper -The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a - convenient, rapid and memory efficient manner. -""" +description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large + datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" sources = ['generic-%(namelower)s-%(version)s.tar.gz'] source_urls = ['http://csg.sph.umich.edu/abecasis/Metal/download/'] @@ -18,7 +15,7 @@ toolchainopts = {'pic': True} patches = ['Metal-%(version)s_Makefile.patch'] -skipsteps=['configure'] +skipsteps = ['configure'] buildopts = 'all' diff --git a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb index 8523144221..947de950b4 100644 --- a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb @@ -28,4 +28,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb index 50e766c0ce..c6a015a815 100644 --- a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -24,8 +24,10 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] dependencies = [ ('zlib', '1.2.8'), # This app also depends in openblas -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), + ] # firt move to folder libStatGen to run make clean && make diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index ba77602cd4..4c07b64293 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -5,7 +5,7 @@ version = '2.0.0' homepage = 'http://icl.cs.utk.edu/magma/' description = """The MAGMA project aims to develop a dense linear algebra library similar to -LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} @@ -15,7 +15,7 @@ source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] patches = [('magma-2.0.0.patch')] -builddependencies = [ ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] +builddependencies = [('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb index 08d2e9759c..73545656c9 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb index 221229e3a6..763ccba836 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb index 5d19338ab3..dab01e8798 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb index b6703cee30..4aa55f0033 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index ee1c589750..eb46a80abe 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb index 1673c64e60..62f71cc876 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb index 23fd809bd7..1b74bd9124 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb index 3a9a7c7e64..91ed160613 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb @@ -4,9 +4,9 @@ name = 'motif' version = '2.3.5' homepage = 'http://motif.ics.com/' -description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building - applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. - It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for + building applications that follow that specification under the X Window System on Unix and other POSIX-compliant + systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" toolchain = {'name': 'foss', 'version': '2016a'} # use -O1 to dance around icc segfaulting @@ -42,4 +42,4 @@ sanity_check_paths = { 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb index 2b7c9b71bd..fb05915a84 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -21,7 +21,7 @@ parallel = 1 buildopts = ' CC="$CC"' -files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] +files_to_copy = [(['mrfast'], 'bin'), "LICENSE"] sanity_check_paths = { 'files': ["bin/mrfast"], diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb index 086efed6cd..1bc0838af6 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -21,7 +21,7 @@ parallel = 1 buildopts = ' CC="$CC"' -files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] +files_to_copy = [(['mrfast'], 'bin'), "LICENSE"] sanity_check_paths = { 'files': ["bin/mrfast"], diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb index 7da0c48dde..e58c648eee 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -24,7 +24,7 @@ patches = ['mrsFAST-%(version)s-intel-compiler.patch'] parallel = 1 -files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] +files_to_copy = [(['mrsfast'], 'bin'), "Changelog"] sanity_check_paths = { 'files': ["bin/mrsfast"], diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb index fda1eaa51f..933177a5af 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -24,7 +24,7 @@ patches = ['mrsFAST-%(version)s-intel-compiler.patch'] parallel = 1 -files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] +files_to_copy = [(['mrsfast'], 'bin'), "Changelog"] sanity_check_paths = { 'files': ["bin/mrsfast"], -- GitLab From 78a9d5a38696a3871b1c9a30cc838f5a3a6a2274 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 9 Mar 2017 17:42:47 +1030 Subject: [PATCH 448/818] PileOMeth added --- .../p/PileOMeth/PileOMeth-0.1.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb new file mode 100644 index 0000000000..af4dcdba98 --- /dev/null +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +### + +easyblock = 'MakeCp' + +name = 'PileOMeth' +version = '0.1.11' + +homepage = 'https://github.com/dpryan79/PileOMeth' +description = """PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments. +PileOMeth extracts per-base methylation metrics from them. +PileOMeth requires an indexed fasta file containing the reference genome as well. +""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(version)s.zip'] +source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] + +dependencies = [ + ('HTSlib', '1.2.1', '', ('foss', '2017a')) +] + +files_to_copy = [ + (["PileOMeth"], "bin"), "*.c", "*.h" +] + +sanity_check_paths = { + 'files': ["bin/PileOMeth"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e1b83120c8d9ac9a9753f21956a8e66d731a0242 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 09:40:33 +0100 Subject: [PATCH 449/818] miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 8a8e1422a7..7f489ba651 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -20,10 +20,13 @@ dependencies = [ ('randfold', '2.0.1'), # also provides SQUID ] -install_cmd = "chmod a+x mirdeep*/src/*.pl && cp -a mirdeep*/src %(installdir)s/bin" +install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " + +# scripts include a hard check for a file called 'install_successful' in the install directory... +install_cmd += "touch %(installdir)s/install_successful" sanity_check_paths = { - 'files': ['bin/make_html.pl'], + 'files': ['bin/mapper.pl', 'bin/miRDeep2.pl'], 'dirs': [], } -- GitLab From a2c62538a6049740584c8c668082799db24e404f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 9 Mar 2017 10:45:09 +0100 Subject: [PATCH 450/818] added GFOLD easyconfig for goolf and intel --- .../g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb | 34 +++++++++++++++++++ .../g/GFOLD/GFOLD-1.1.4-intel-2016a.eb | 34 +++++++++++++++++++ .../g/GFOLD/gfold-1.1.4-makefile.patch | 18 ++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..8d11408e6b --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GFOLD' +version = '1.1.4' + +homepage = 'http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html' +description = 'Generalized fold change for ranking differentially expressed genes from RNA-seq data' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://bitbucket.org/feeldead/gfold/downloads/'] +sources = ['%(namelower)s.V%(version)s.tar.gz'] + +patches = ['gfold-%(version)s-makefile.patch'] + +dependencies = [ + ('GSL', '1.16'), +] + +files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..3b289b47ea --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GFOLD' +version = '1.1.4' + +homepage = 'http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html' +description = 'Generalized fold change for ranking differentially expressed genes from RNA-seq data' + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/feeldead/gfold/downloads/'] +sources = ['%(namelower)s.V%(version)s.tar.gz'] + +patches = ['gfold-%(version)s-makefile.patch'] + +dependencies = [ + ('GSL', '1.16'), +] + +files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch new file mode 100644 index 0000000000..15699d96ba --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -0,0 +1,18 @@ +fix the hardcoded compiler + +diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile +--- gfold.V1.1.4.orig/Makefile 2015-05-24 01:47:13.000000000 +0200 ++++ gfold.V1.1.4/Makefile 2017-03-09 10:32:23.919031000 +0100 +@@ -5,10 +5,10 @@ + all: program + + debug: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc +- g++ -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} -Wall -g main.cc -o gfold -lgsl -lgslcblas + + program: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc +- g++ -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas + + docu: doc/gfold.pod + pod2man doc/gfold.pod > doc/gfold.man -- GitLab From 4f92b9fa68fb297f350a600d382f67e09cb723f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:04:34 +0100 Subject: [PATCH 451/818] adding easyconfigs: GDAL-2.1.3-foss-2016b-Python-2.7.12.eb --- .../GDAL-2.1.3-foss-2016b-Python-2.7.12.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0f954c1b05 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +#patches = ['GDAL-2.1.2_fix-vrtsources.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +# there is a bug in the build system causing the build with libtool to fail for the moment +# (static library is also missing because of this) +#configopts += ' --without-libtool' + +#buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From b7eee70912a1b3dc6722c933b62449e870a44ffa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:04:52 +0100 Subject: [PATCH 452/818] adding easyconfigs: PROJ-4.9.3-foss-2016b.eb --- .../p/PROJ/PROJ-4.9.3-foss-2016b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb new file mode 100644 index 0000000000..7c6ed61f58 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-55-44 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 94.84, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", 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--enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 4259625, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmpNuI7H2/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891344, + "total_memory": 64303, +}] -- GitLab From 6e355d309317b055b0623b27a22b1a1ff72f6f2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:07:54 +0100 Subject: [PATCH 453/818] adding easyconfigs: GEOS-3.6.1-foss-2016b-Python-2.7.12.eb, SWIG-3.0.11-foss-2016b-Python-2.7.12.eb --- .../GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 55 +++++++++++++++++++ .../SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 47 ++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ff17f25dff --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,55 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_14-08-23 +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.12')] + +builddependencies = [('SWIG', '3.0.11', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' + +# Build statistics +buildstats = [{ + "build_time": 431.44, + "command_line": 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'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 13415865, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmpb49pQv/gcc", + "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", + "timestamp": 1488892103, + "total_memory": 64303, +}] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bd7c62c123 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_14-01-11 +name = 'SWIG' +version = '3.0.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "build_time": 62.35, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 5103738, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmpn3FMec/gcc", + "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", + "timestamp": 1488891671, + "total_memory": 64303, +}] -- GitLab From 222de2e3bcc8228b30cb935fa60a8e9e27fa2b9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:08:12 +0100 Subject: [PATCH 454/818] adding easyconfigs: libspatialindex-1.8.5-foss-2016b.eb --- .../libspatialindex-1.8.5-foss-2016b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb new file mode 100644 index 0000000000..33443350fb --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -0,0 +1,46 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-58-08 +easyblock = 'ConfigureMake' + +name = 'libspatialindex' +version = '1.8.5' + +homepage = 'http://libspatialindex.github.io' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/libspatialindex/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.a', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 143.61, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 5693279, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmp07Ujmt/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891488, + "total_memory": 64303, +}] -- GitLab From 6191d257e6b77b205173a2ef627a9a8f8b81a01d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:08:50 +0100 Subject: [PATCH 455/818] adding easyconfigs: FreeXL-1.0.2-foss-2016b.eb --- .../f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb new file mode 100644 index 0000000000..1e91b6e6f0 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -0,0 +1,49 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-59-03 +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.2' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.7.1')] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] + } + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 55.18, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 205319, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmp6qSQU6/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891543, + "total_memory": 64303, +}] -- GitLab From 67d6b752d1bfb4e6abe3a7596f966e6a62de5e45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:12:37 +0100 Subject: [PATCH 456/818] remove buildstats --- .../p/PROJ/PROJ-4.9.3-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index 7c6ed61f58..bd62ff7fdd 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -29,29 +29,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 94.84, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 4259625, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpNuI7H2/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891344, - "total_memory": 64303, -}] -- GitLab From 8367087c08ef9ae7372e516dc3c7952708051cfa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:13:40 +0100 Subject: [PATCH 457/818] remove buildstats --- .../GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 26 ------------------- .../SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 26 ------------------- 2 files changed, 52 deletions(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb index ff17f25dff..95a33702aa 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -27,29 +27,3 @@ sanity_check_paths = { } moduleclass = 'math' - -# Build statistics -buildstats = [{ - "build_time": 431.44, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 13415865, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpb49pQv/gcc", - "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", - "timestamp": 1488892103, - "total_memory": 64303, -}] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb index bd7c62c123..ef67967e6e 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -19,29 +19,3 @@ dependencies = [ ] moduleclass = 'devel' - -# Build statistics -buildstats = [{ - "build_time": 62.35, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 5103738, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpn3FMec/gcc", - "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", - "timestamp": 1488891671, - "total_memory": 64303, -}] -- GitLab From b5c23e38fc28cceee226e97635e52133ab9ecc3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:13:40 +0100 Subject: [PATCH 458/818] remove buildstats --- .../libspatialindex-1.8.5-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb index 33443350fb..6393dbd967 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -18,29 +18,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 143.61, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 5693279, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmp07Ujmt/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891488, - "total_memory": 64303, -}] -- GitLab From 1cf8d4ec36e74b4eedd969376ccce569e18fd13f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:14:58 +0100 Subject: [PATCH 459/818] remove buildstats --- .../f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index 1e91b6e6f0..f20ffb2db6 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -21,29 +21,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 55.18, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 205319, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmp6qSQU6/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891543, - "total_memory": 64303, -}] -- GitLab From eb3e66959e2ab315db0c3819b436b186463b65a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:22:06 +0100 Subject: [PATCH 460/818] remove commented out lines --- .../g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb index 0f954c1b05..bc2162b8fb 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb @@ -16,8 +16,6 @@ toolchainopts = {'usempi': True} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] -#patches = ['GDAL-2.1.2_fix-vrtsources.patch'] - dependencies = [ ('Python', '2.7.12'), ('netCDF', '4.4.1.1'), @@ -38,11 +36,6 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -# there is a bug in the build system causing the build with libtool to fail for the moment -# (static library is also missing because of this) -#configopts += ' --without-libtool' - -#buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -- GitLab From 9795a9c4c7c3d4ba24cbd1f0ace84bb7b426f937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:00:51 +0100 Subject: [PATCH 461/818] remove 'Built with' comments --- .../easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 1 - easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb | 1 - .../easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb index 95a33702aa..02e7eb0e40 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_14-08-23 easyblock = 'ConfigureMake' name = 'GEOS' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index bd62ff7fdd..7b1bb021f3 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-55-44 ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb index ef67967e6e..645b771837 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_14-01-11 name = 'SWIG' version = '3.0.11' versionsuffix = '-Python-%(pyver)s' -- GitLab From 85ee43bb91417d48bb753d3e85f0427c50f03069 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:01:56 +0100 Subject: [PATCH 462/818] remove 'Built with' comment --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index f20ffb2db6..2775a19a49 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-59-03 easyblock = 'ConfigureMake' name = 'FreeXL' -- GitLab From 62fc9ea965433cb32529fb9b5e058a6fe5805367 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:03:24 +0100 Subject: [PATCH 463/818] remove 'Built with' comment --- .../l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb index 6393dbd967..5ff79fa5a7 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-58-08 easyblock = 'ConfigureMake' name = 'libspatialindex' -- GitLab From 7206a55c12c3eb2b748b83b94957030601c762b5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 13:22:27 +0100 Subject: [PATCH 464/818] add ${CXXFLAGS} to the patch file --- easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch index 15699d96ba..08f6097072 100644 --- a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -8,11 +8,11 @@ diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile debug: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc - g++ -Wall -g main.cc -o gfold -lgsl -lgslcblas -+ ${CXX} -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas program: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc - g++ -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas -+ ${CXX} -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas docu: doc/gfold.pod pod2man doc/gfold.pod > doc/gfold.man -- GitLab From 6efe46cb2ad1f6a29fb5a8268ff27a9fb7dd9c5e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 13:22:50 +0100 Subject: [PATCH 465/818] update the patch comment --- easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch index 08f6097072..23ba52ac63 100644 --- a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -1,4 +1,4 @@ -fix the hardcoded compiler +fix the hardcoded compiler and use ${CXXFLAGS} diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile --- gfold.V1.1.4.orig/Makefile 2015-05-24 01:47:13.000000000 +0200 -- GitLab From ff1bba6485cfb033f60e7a58f5442b49ff854d0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:49:40 +0100 Subject: [PATCH 466/818] fix minor style issue --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index 2775a19a49..b7981e18c5 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.7.1')] sanity_check_paths = { 'files': ['lib/libfreexl.a'], 'dirs': [] - } +} moduleclass = 'lib' -- GitLab From 76eec10c26deba272148df8e3229eab11166444c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:09:46 +0100 Subject: [PATCH 467/818] fix shebang in miRDeep2 Perl scripts --- easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 7f489ba651..de73467658 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " +install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From 31b0580e2f82fe48ac5901484363f8d60bcf4fdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:34:50 +0100 Subject: [PATCH 468/818] adding easyconfigs: flex-2.6.3-GCCcore-5.4.0.eb, M4-1.4.18-GCCcore-5.4.0.eb, help2man-1.47.4-GCCcore-5.4.0.eb --- .../f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 23 +++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 19 ++++++++++++++ .../m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 25 +++++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..5044907def --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -0,0 +1,23 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('binutils', '2.26'), + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..7b53bd8797 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..345402c605 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b35c28b493af2a252f41971c1d3b492a7000460c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:36:09 +0100 Subject: [PATCH 469/818] adding easyconfigs: GDAL-2.1.3-intel-2016b-Python-2.7.12.eb --- .../GDAL-2.1.3-intel-2016b-Python-2.7.12.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..015f10d595 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From 59df1b140f4267a1b1abfac49143a39edf87063c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:38:46 +0100 Subject: [PATCH 470/818] adding easyconfigs: QCA-2.1.3-intel-2016b.eb --- .../q/QCA/QCA-2.1.3-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb new file mode 100644 index 0000000000..2b7816fd3c --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.3' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/src/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From f4c13b9569fe8b33ab8a8ebb5a38f51846cad3a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:39:12 +0100 Subject: [PATCH 471/818] adding easyconfigs: QJson-0.9.0-intel-2016b.eb --- .../q/QJson/QJson-0.9.0-intel-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb new file mode 100644 index 0000000000..44efa4db59 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7'), +] +builddependencies = [ + ('CMake', '3.7.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson.%s' % SHLIB_EXT], + 'dirs': ['include/qjson', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From 8c335a1b251205d9c90948cbdff9deca9386b26a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:39:36 +0100 Subject: [PATCH 472/818] adding easyconfigs: QScintilla2-2.10-intel-2016b-Python-2.7.12.eb --- ...intilla2-2.10-intel-2016b-Python-2.7.12.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..be392c7b0b --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'QScintilla2' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla2-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +start_dir = 'Qt4Qt5' + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@\$\$\[QT_INSTALL_LIBS\]@%(installdir)s/lib@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_HEADERS\]@%(installdir)s/include@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_TRANSLATIONS\]@%(installdir)s/trans@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_DATA\]@%(installdir)s/data@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_HOST_DATA\]@%(installdir)s/data@g' qscintilla.pro && " +prebuildopts += "qmake qscintilla.pro && " + +buildopts = 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"' + +python_bindings_install_cmd = "cd ../Python && mkdir -p %(installdir)s/share/sip/PyQt4 && " +python_bindings_install_cmd += "python configure.py --destdir %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 --qsci-sipdir %(installdir)s/share/sip/PyQt4 --qsci-incdir %(installdir)s/include --qsci-libdir %(installdir)s/lib --pyqt-sipdir $EBROOTPYQT/share/sip/PyQt4 --apidir %(installdir)s/qsci/api/python --no-stubs && " +python_bindings_install_cmd += "make && make install && cd %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 && " +python_bindings_install_cmd += "for x in $(ls $EBROOTPYQT/lib/python2.7/site-packages/PyQt4); do ln -s $EBROOTPYQT/lib/python2.7/site-packages/PyQt4/$x; done && " +python_bindings_install_cmd += "rm __init__.py* && touch __init__.py" +postinstallcmds = [python_bindings_install_cmd] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libqscintilla2_qt4.so'], + 'dirs': ['include/Qsci', 'lib/python%(pyshortver)s/site-packages/PyQt4', 'qsci/api/python', 'share/sip/PyQt4', 'trans'], +} + +sanity_check_commands = ["python -c 'import PyQt4.Qsci'"] + +moduleclass = 'vis' -- GitLab From 8a542052a3ba44588900ab6efbc20a18a457e8a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:42:02 +0100 Subject: [PATCH 473/818] adding easyconfigs: QGIS-2.14.12-intel-2016b-Python-2.7.12.eb --- .../QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..abd1b36a0c --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.14.12' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-2.14.12.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla2 must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla2', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +configopts = '-DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson -DCMAKE_PREFIX_PATH=$EBROOTQT -DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so -DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4' + +buildopts = "VERBOSE=1 V=1" + +sanity_check_paths = { + 'files': ['bin/qgis'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From bb02a546f8c3ed7ac96345ed57cb7ccf8cdfc9d5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 14:52:18 +0100 Subject: [PATCH 474/818] style fixes --- .../disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 08032c986d..816f774c49 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -26,8 +26,10 @@ dependencies = [ # this application provides a python implementation and a C++ implementation # in the postinstallcmds we compile the C++ version -postinstallcmds = ['$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', - 'cp disambiguate %(installdir)s/bin/'] +postinstallcmds = [ + '$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/' +] # workaround to avoid the import sanity check options = {'modulename': 'os'} -- GitLab From 7101d3a09bda45ed7591d2231f16a6e72148ec07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 16:42:59 +0100 Subject: [PATCH 475/818] update QScintilla easyconfig to use QScintilla easyblock, add easyconfig for QScintilla 2.9.4 --- ...cintilla-2.10-intel-2016b-Python-2.7.12.eb | 21 ++++++++ ...ntilla-2.10_fix-link-python-bindings.patch | 14 +++++ ...intilla-2.9.4-intel-2016b-Python-2.7.12.eb | 21 ++++++++ ...tilla-2.9.4_fix-link-python-bindings.patch | 14 +++++ ...intilla2-2.10-intel-2016b-Python-2.7.12.eb | 52 ------------------- 5 files changed, 70 insertions(+), 52 deletions(-) create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch delete mode 100644 easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a974a1c6ac --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch new file mode 100644 index 0000000000..cca6cde624 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch @@ -0,0 +1,14 @@ +add missing link to QScintilla library to correctly build Python bindings + +author: Kenneth Hoste (HPC-UGent) +--- QScintilla_gpl-2.10/Python/configure.py.orig 2017-03-08 14:29:36.344465661 +0100 ++++ QScintilla_gpl-2.10/Python/configure.py 2017-03-08 14:36:00.439001287 +0100 +@@ -1510,7 +1510,7 @@ + + libs = qmake_config.get('LIBS') + if libs: +- pro.write('LIBS += %s\n' % libs) ++ pro.write('LIBS += %s -lqscintilla2_qt4\n' % libs) + + if not opts.static: + pro.write(''' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..e3f0cde600 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch new file mode 100644 index 0000000000..3abd6f5965 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch @@ -0,0 +1,14 @@ +add missing link to QScintilla library to correctly build Python bindings + +author: Kenneth Hoste (HPC-UGent) +--- QScintilla_gpl-2.9.4/Python/configure.py.orig 2017-03-08 14:29:36.344465661 +0100 ++++ QScintilla_gpl-2.9.4/Python/configure.py 2017-03-08 14:36:00.439001287 +0100 +@@ -1510,7 +1510,7 @@ + + libs = qmake_config.get('LIBS') + if libs: +- pro.write('LIBS += %s\n' % libs) ++ pro.write('LIBS += %s -lqscintilla2\n' % libs) + + if not opts.static: + pro.write(''' diff --git a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb deleted file mode 100644 index be392c7b0b..0000000000 --- a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'QScintilla2' -version = '2.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.riverbankcomputing.com/software/qscintilla' -description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" - -toolchain = {'name': 'intel', 'version': '2016b'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s/QScintilla-%(version)s/'] -sources = ['QScintilla_gpl-%(version)s.tar.gz'] - -patches = ['QScintilla2-%(version)s_fix-link-python-bindings.patch'] - -dependencies = [ - ('Python', '2.7.12'), - ('PyQt', '4.12', versionsuffix), -] - -start_dir = 'Qt4Qt5' - -skipsteps = ['configure'] - -prebuildopts = "sed -i 's@\$\$\[QT_INSTALL_LIBS\]@%(installdir)s/lib@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_HEADERS\]@%(installdir)s/include@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_TRANSLATIONS\]@%(installdir)s/trans@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_DATA\]@%(installdir)s/data@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_HOST_DATA\]@%(installdir)s/data@g' qscintilla.pro && " -prebuildopts += "qmake qscintilla.pro && " - -buildopts = 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"' - -python_bindings_install_cmd = "cd ../Python && mkdir -p %(installdir)s/share/sip/PyQt4 && " -python_bindings_install_cmd += "python configure.py --destdir %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 --qsci-sipdir %(installdir)s/share/sip/PyQt4 --qsci-incdir %(installdir)s/include --qsci-libdir %(installdir)s/lib --pyqt-sipdir $EBROOTPYQT/share/sip/PyQt4 --apidir %(installdir)s/qsci/api/python --no-stubs && " -python_bindings_install_cmd += "make && make install && cd %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 && " -python_bindings_install_cmd += "for x in $(ls $EBROOTPYQT/lib/python2.7/site-packages/PyQt4); do ln -s $EBROOTPYQT/lib/python2.7/site-packages/PyQt4/$x; done && " -python_bindings_install_cmd += "rm __init__.py* && touch __init__.py" -postinstallcmds = [python_bindings_install_cmd] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_paths = { - 'files': ['lib/libqscintilla2_qt4.so'], - 'dirs': ['include/Qsci', 'lib/python%(pyshortver)s/site-packages/PyQt4', 'qsci/api/python', 'share/sip/PyQt4', 'trans'], -} - -sanity_check_commands = ["python -c 'import PyQt4.Qsci'"] - -moduleclass = 'vis' -- GitLab From 058dd65ade21434c77d9b72656ae5863f2eaf3c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 16:53:26 +0100 Subject: [PATCH 476/818] QScintilla2 -> QScintilla, clean up configopts, enhance sanity check for QGIS --- .../QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index abd1b36a0c..d97a872052 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -28,8 +28,8 @@ dependencies = [ ('expat', '2.2.0'), ('QCA', '2.1.3'), ('PyQt', '4.12', versionsuffix), - # QScintilla2 must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 - ('QScintilla2', '2.10', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), ] @@ -41,13 +41,16 @@ builddependencies = [ separate_build_dir = True -configopts = '-DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson -DCMAKE_PREFIX_PATH=$EBROOTQT -DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so -DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4' - -buildopts = "VERBOSE=1 V=1" +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4" sanity_check_paths = { - 'files': ['bin/qgis'], - 'dirs': [], + 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_networkanalysis.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], } moduleclass = 'geo' -- GitLab From 358985ef2ee5d86074951462c0d8a6c3a3533eb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 17:00:42 +0100 Subject: [PATCH 477/818] add patch for QGIS 2.14.12 --- .../QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 2 +- .../q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index d97a872052..9b31165cdc 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True, 'cstd': 'gnu++11'} source_urls = ['http://qgis.org/downloads/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['QGIS-2.14.12.patch'] +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] dependencies = [ ('Qt', '4.8.7'), diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch new file mode 100644 index 0000000000..2eb3299a7d --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch @@ -0,0 +1,14 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +--- qgis-2.14.12/cmake/SIPMacros.cmake.orig 2017-03-09 12:57:14.037320233 +0100 ++++ qgis-2.14.12/cmake/SIPMacros.cmake 2017-03-09 13:05:55.739057294 +0100 +@@ -102,7 +102,7 @@ + ENDIF(PEDANTIC) + + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_abs_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} -I$ENV{EBROOTPYQT}/share/sip/PyQt4 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) -- GitLab From 616fe782803b18052ff11d6a1fc6eba545cb57e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 17:37:13 +0100 Subject: [PATCH 478/818] fix $EBROOT for QScintilla --- .../q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index 9b31165cdc..43245eb873 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -43,8 +43,8 @@ separate_build_dir = True # specify locations that CMake can't figure out correctly configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " -configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so " -configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4" +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt4" sanity_check_paths = { 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, -- GitLab From c326a3be445d0ad2f149747707daf4addd88ff7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:41:37 +0100 Subject: [PATCH 479/818] adding easyconfigs: libspatialite-4.3.0a-foss-2016b.eb --- .../libspatialite-4.3.0a-foss-2016b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb new file mode 100644 index 0000000000..c87d185cc1 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.6.1', '-Python-2.7.12'), + ('SQLite', '3.13.0'), + ('PROJ', '4.9.3'), +] + +builddependencies = [('CMake', '3.7.1')] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} + +moduleclass = 'lib' -- GitLab From de1032dfcb6d247eb98e23a8f63146c82dc6f57d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:56:54 +0100 Subject: [PATCH 480/818] adding easyconfigs: PyQt-4.12-foss-2016b-Python-2.7.12.eb, SIP-4.19-foss-2016b-Python-2.7.12.eb --- .../PyQt-4.12-foss-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ .../SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb | 30 +++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f8e50daad2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] +sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('SIP', '4.19', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..be020214d2 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.12')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From fccbb78c76415fc8bafa07811b51c091e3bcf9a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:57:53 +0100 Subject: [PATCH 481/818] also enable installation of SIP files in PyQt 4.12 easyconfig used intel/2016b --- .../easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb index 9ea42178d7..8afd4b1225 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = "configure-ng.py --confirm-license" configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " -configopts += " --no-sip-files" +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" options = {'modulename': '%(name)s%(version_major)s'} -- GitLab From f1dba5919c4d1a1081412e33b37fa8d863b53904 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:00:15 +0100 Subject: [PATCH 482/818] include binutils as build dep in flex/help2man/M4 easyconfigs using GCCcore/5.4.0 --- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 3 ++- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 5 +++++ easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 3 +++ 3 files changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index 5044907def..fea2687908 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -15,9 +15,10 @@ checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] dependencies = [('M4', '1.4.18')] builddependencies = [ - ('binutils', '2.26'), ('Bison', '3.0.4'), ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 7b53bd8797..0d730043fb 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -11,6 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), +] + sanity_check_paths = { 'files': ['bin/help2man'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 345402c605..c1c1439bf3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -13,6 +13,9 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" -- GitLab From dfb169134cb268f9ae36f937ba2e650e605ef173 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:05:28 +0100 Subject: [PATCH 483/818] adding easyconfigs: QwtPolar-1.1.1-foss-2016b.eb, Qwt-6.1.3-foss-2016b.eb --- .../easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb | 29 +++++++++++++++++++ .../q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb new file mode 100644 index 0000000000..f2b00bf192 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.3' + +homepage = 'http://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qt', '4.8.7'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@QWT_INSTALL_PREFIX[ ]*=.*@QWT_INSTALL_PREFIX = %(installdir)s@g' qwtconfig.pri && " +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb new file mode 100644 index 0000000000..bf12b1ad5e --- /dev/null +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'QwtPolar' +version = '1.1.1' + +homepage = 'http://qwtpolar.sourceforge.net/' +description = "The QwtPolar library contains classes for displaying values on a polar coordinate system." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qwt', '6.1.3'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@INSTALL_PREFIX[ ]*=.*@INSTALL_PREFIX = %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " +prebuildopts += "qmake qwtpolar.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwtpolar.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' -- GitLab From cf4446f582499934c66770414128fd17c3b1f804 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:17:17 +0100 Subject: [PATCH 484/818] adding easyconfigs: QJson-0.9.0-foss-2016b.eb --- .../q/QJson/QJson-0.9.0-foss-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb new file mode 100644 index 0000000000..32b2329111 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7'), +] +builddependencies = [ + ('CMake', '3.7.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson.%s' % SHLIB_EXT], + 'dirs': ['include/qjson', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From b280b34714182becf501f1b79cb4f7c83d335a63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:17:47 +0100 Subject: [PATCH 485/818] adding easyconfigs: QCA-2.1.3-foss-2016b.eb --- .../easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb new file mode 100644 index 0000000000..4a94646890 --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.3' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/src/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From c21818052a0b1ca09202778fa7b6cb5361cb15aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:13:51 +0100 Subject: [PATCH 486/818] adding easyconfigs: QScintilla-2.10-foss-2016b-Python-2.7.12.eb, QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb --- ...Scintilla-2.10-foss-2016b-Python-2.7.12.eb | 21 +++++++++++++++++++ ...cintilla-2.9.4-foss-2016b-Python-2.7.12.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..13dd45e489 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f6edee2ee2 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' -- GitLab From 6b206c39bf1a05d066bf894be6ff0838dbe84ee8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:19:58 +0100 Subject: [PATCH 487/818] {geo}[foss/2016b] QGIS v2.18.4 --- .../QGIS-2.18.4-foss-2016b-Python-2.7.12.eb | 56 +++++++++++++++++++ .../q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch | 14 +++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f6d58e7bf7 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.18.4' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt4" + +sanity_check_paths = { + 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_networkanalysis.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch new file mode 100644 index 0000000000..5d04066fb1 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch @@ -0,0 +1,14 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +--- qgis-2.18.4/cmake/SIPMacros.cmake.orig 2017-03-08 17:44:20.698576501 +0100 ++++ qgis-2.18.4/cmake/SIPMacros.cmake 2017-03-08 17:46:39.110172584 +0100 +@@ -96,7 +96,7 @@ + ADD_DEFINITIONS( /bigobj ) + ENDIF(MSVC) + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_abs_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} -I$ENV{EBROOTPYQT}/share/sip/PyQt4 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) -- GitLab From ad89278bbc144ca83fef7955ceb5580c69721100 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:37:17 +0100 Subject: [PATCH 488/818] also check with Tcl module syntax, Lua is the default in EasyBuild v3.x --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 13ca5c0612..07cebed738 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,11 +4,11 @@ env: matrix: - ENV_MOD_VERSION=3.2.10 EASYBUILD_MODULES_TOOL=EnvironmentModulesC EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=5.8 - - LMOD_VERSION=5.8 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=5.8 EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=6.6.3 - - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=7.0 - - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Tcl matrix: # mark build as finished as soon as job has failed fast_finish: true -- GitLab From 64f3c1865cccb676751b50727b46261ffe3b92e5 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 12:25:14 +1030 Subject: [PATCH 489/818] Style fixed --- .../{PileOMeth-0.1.11.eb => PileOMeth-0.1.11-foss-2016b.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PileOMeth/{PileOMeth-0.1.11.eb => PileOMeth-0.1.11-foss-2016b.eb} (87%) diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb similarity index 87% rename from easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb rename to easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb index af4dcdba98..edf4ca1f37 100644 --- a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb @@ -19,17 +19,17 @@ description = """PileOMeth processes a coordinate-sorted and indexed BAM or CRAM PileOMeth extracts per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'foss', 'version': '2016b'} sources = ['%(version)s.zip'] source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] dependencies = [ - ('HTSlib', '1.2.1', '', ('foss', '2017a')) + ('HTSlib', '1.2.1') ] files_to_copy = [ - (["PileOMeth"], "bin"), "*.c", "*.h" + (["PileOMeth"], "bin"), ] sanity_check_paths = { -- GitLab From c0d6c2c7a08c93059ce58bcb0970daac4738744d Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 12:27:59 +1030 Subject: [PATCH 490/818] HTSlib added --- .../h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb new file mode 100644 index 0000000000..66babc415c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -0,0 +1,39 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Acknowledgement:: +# Original Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +## + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.2.1' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 94d3b3ff4ea86240bfbb2b4a06361d80410076f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:27:41 +0100 Subject: [PATCH 491/818] also copy Rfam_for_miRDeep.fa to mirDeep2 bin directory --- easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index de73467658..466cd04f4d 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -22,6 +22,7 @@ dependencies = [ install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s/bin/ && " # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From e5f020956911d15e337bfa2f7a0fd140843d84f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:36:31 +0100 Subject: [PATCH 492/818] adding easyconfigs: requests-2.13.0-foss-2016b-Python-2.7.12.eb, requests-2.13.0-intel-2016b-Python-2.7.12.eb --- ...equests-2.13.0-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ ...quests-2.13.0-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2546a92787 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3d08d7d724 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From bdee396c0c108c92a0ea57f8540ed45571e7aa4f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:46:42 +0100 Subject: [PATCH 493/818] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb index a2bf4ab035..b3d257608f 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -33,4 +33,8 @@ configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_ configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 398343a8cdb5277b46ab50061bb26bf009c7126e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:47:44 +0100 Subject: [PATCH 494/818] fix PostgreSQL homepage + minor style fixes --- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 15 +++++++-------- .../PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 10 ++++++---- .../PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 10 ++++++---- .../PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb | 8 ++++---- 4 files changed, 23 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index b694510474..8b0668a68f 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PostgreSQL' version = '9.3.5' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -18,18 +18,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] - -java = 'Java' -javaver = '1.7.0_60' - dependencies = [ - (java, javaver, '', True), + ('Java', '1.7.0_60', '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.2'), ('flex', '2.5.39'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index a7d2b6c4a0..6302a94b89 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.4.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -19,15 +19,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index 46e78c9224..c49c4abba6 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -19,15 +19,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb index 8f8750717c..67556bd516 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.6.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -19,13 +19,13 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016b'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.12'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] builddependencies = [ -- GitLab From 51bbcc9046b2b2825a455be134d694e4bb7ba615 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:48:03 +0100 Subject: [PATCH 495/818] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb index f56b457e0d..99a4b3d8d6 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb @@ -33,4 +33,8 @@ configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-x configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 526cbfca04174161d69fd149e9e407c9e313cc56 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:50:15 +0100 Subject: [PATCH 496/818] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index a263fbc4af..c111bdfea0 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -38,4 +38,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 7c1a1484d29b05d06349acaa11a8829e87a1caf0 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:51:16 +0100 Subject: [PATCH 497/818] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb index 4f55d64d72..a90994c1ab 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -38,4 +38,8 @@ configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdi configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From eaa6b52cb1d25ecd15bb5ac553cbc3771b02b9fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:53:30 +0100 Subject: [PATCH 498/818] adding easyconfigs: psycopg2-2.7-intel-2016b-Python-2.7.12.eb, psycopg2-2.7-foss-2016b-Python-2.7.12.eb, PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb, PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb --- ...stgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb | 46 +++++++++++++++++++ ...tgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb | 46 +++++++++++++++++++ .../psycopg2-2.7-foss-2016b-Python-2.7.12.eb | 25 ++++++++++ .../psycopg2-2.7-intel-2016b-Python-2.7.12.eb | 25 ++++++++++ 4 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..537ebb2758 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.24.0'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9d98aaa673 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.24.0'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..948a2bd8f6 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://initd.org/psycopg/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PostgreSQL', '9.6.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3ac0511ce1 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://initd.org/psycopg/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PostgreSQL', '9.6.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From ba956899575eb5c51c8ef37229213151fdcafad1 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:54:43 +0100 Subject: [PATCH 499/818] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb index 81b811dc89..80a084ac4d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb @@ -36,4 +36,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 412ba617c5167ddb3593007a38cb0820f7c1702a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:56:02 +0100 Subject: [PATCH 500/818] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 9dd615415d..718fb2f36d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -54,4 +54,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 83e7f94a3fea698444e22140da2fc3b7eb97f119 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:56:58 +0100 Subject: [PATCH 501/818] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index b51c955db4..d8466b4858 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -54,4 +54,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From e80f2a6d6aa67ace904af25a62af8efe2646b08a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:57:41 +0100 Subject: [PATCH 502/818] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb index 2ddf7531c8..6d3d2000b8 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb @@ -52,4 +52,8 @@ configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX1 configopts += ' --with-xft-libdir=$EBROOTX11/lib' configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 17e252c4b0b1c3fcb5830d97cb42bcd636e394f8 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 11:09:37 +0100 Subject: [PATCH 503/818] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index a8ab1f540d..f662b0deda 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -42,4 +42,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From e0b7bd52bbfda4bec6fca382313bd6b7825276ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 11:11:42 +0100 Subject: [PATCH 504/818] fix location for Rfam_for_miRDeep.fa --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 466cd04f4d..83e5129dff 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -22,7 +22,7 @@ dependencies = [ install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' -install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s/bin/ && " +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s && " # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From f2326dc17da8f931f34c89935d2c5572dd788645 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 11:16:20 +0100 Subject: [PATCH 505/818] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 5801dbe265..6073d0e56c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -56,4 +56,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 7487ef4bd7ec0e279be25ab423ec2b9be38f1e38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 11:21:12 +0100 Subject: [PATCH 506/818] detect use of '$root', which is not compatible with module files in Lua syntax --- test/easyconfigs/easyconfigs.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 551695c259..993e9395ba 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -235,6 +235,11 @@ def template_easyconfig_test(self, spec): self.assertTrue(name, app.name) self.assertTrue(ec['version'], app.version) + # make sure that $root is not used, since it is not compatible with module files in Lua syntax + res = re.findall('.*\$root.*', ec.rawtxt, re.M) + error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" + self.assertFalse(res, error_msg % res) + # make sure all patch files are available specdir = os.path.dirname(spec) specfn = os.path.basename(spec) -- GitLab From 667725596613b792b086d6356b7e6cdc7c22326a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 10 Mar 2017 11:57:26 +0100 Subject: [PATCH 507/818] added $CXXFLAGS --- .../disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 816f774c49..7de0a8ea92 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -27,7 +27,7 @@ dependencies = [ # this application provides a python implementation and a C++ implementation # in the postinstallcmds we compile the C++ version postinstallcmds = [ - '$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + '$CXX $CXXFLAGS -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', 'cp disambiguate %(installdir)s/bin/' ] -- GitLab From 75998c8fd4ad81ef8b43d41152800e059a3adc88 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 21:55:20 +1030 Subject: [PATCH 508/818] style fixed --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb index 66babc415c..a58dae978a 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], 'dirs': [], } -- GitLab From d1132ead52ea73d356501e39a3b9b603dffb4c0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 13:12:07 +0100 Subject: [PATCH 509/818] add requests and psycopg2 as dependencies for QGIS --- .../q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index 43245eb873..4878b7d629 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -32,6 +32,8 @@ dependencies = [ ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), ] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 3d0c4aa8ab68e2d7fed93ce83b3f9652a7ad03f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 13:47:15 +0100 Subject: [PATCH 510/818] add requests and psycopg2 as dependencies for QGIS --- .../easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb index f6d58e7bf7..837899aa93 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -32,6 +32,8 @@ dependencies = [ ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), ] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 674ce7782bb9b25ee3721dbe0017218df74cd31b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 14:01:42 +0100 Subject: [PATCH 511/818] avoid use of '$root', replace with '%(installdir)s' --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 10 +++------- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 10 +++------- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 11 +++-------- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 11 +++-------- .../m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 4 +--- .../easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 4 +--- .../easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 4 +--- 7 files changed, 15 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 56456bbd62..4c41ac6ece 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -25,16 +25,12 @@ dependencies = [ separate_build_dir = True -modextravars = { - 'ALPS_ROOT': '$root', -} -modextrapaths = { - 'PYTHONPATH': ['lib/'] -} - sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } +modextravars = {'ALPS_ROOT': '%(installdir)s'} +modextrapaths = {'PYTHONPATH': ['lib/']} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index f21285e25b..3d3e67389f 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -25,16 +25,12 @@ dependencies = [ separate_build_dir = True -modextravars = { - 'ALPS_ROOT': '$root', -} -modextrapaths = { - 'PYTHONPATH': ['lib/'] -} - sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } +modextravars = {'ALPS_ROOT': '%(installdir)s'} +modextrapaths = {'PYTHONPATH': ['lib']} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 21ae128381..6e3b23ba3c 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -31,17 +31,12 @@ postinstallcmds = [ "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s", ] -modextrapaths = { - 'CLASSPATH': 'lib', -} - -modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory -} - sanity_check_paths = { 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], 'dirs': [] } +modextravars = {'MPJ_HOME': '%(installdir)s'} +modextrapaths = {'CLASSPATH': 'lib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 41195e5042..8577e3deb4 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -34,17 +34,12 @@ postinstallcmds = [ "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s", ] -modextrapaths = { - 'CLASSPATH': 'lib', -} - -modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory -} - sanity_check_paths = { 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], 'dirs': [] } +modextravars = {'MPJ_HOME': '%(installdir)s'} +modextrapaths = {'CLASSPATH': 'lib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb index 44efa704ef..973e13d894 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -25,8 +25,6 @@ sanity_check_paths = { 'dirs': ["lib"], } -modextravars = { - 'PERL5LIB': '$root/lib' -} +modextrapaths = {'PERL5LIB': 'lib'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index 77fe169073..c6a5e3fa14 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -31,9 +31,7 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 70198200d8..96ac9d6530 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -31,9 +31,7 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" -- GitLab From 7b5bab1965fb311d42f87d63078aa80dad41820f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Mar 2017 15:25:56 +0200 Subject: [PATCH 512/818] adding easyconfigs: Yasm-1.3.0-foss-2017a.eb, Yasm-1.3.0-intel-2017a.eb --- .../y/Yasm/Yasm-1.3.0-foss-2017a.eb | 31 +++++++++++++++++++ .../y/Yasm/Yasm-1.3.0-intel-2017a.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb new file mode 100644 index 0000000000..bae739cbfa --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb new file mode 100644 index 0000000000..f0db7e8256 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 7ab680ea704aa1db04f7db38635b33a760437b9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Mar 2017 16:56:47 +0200 Subject: [PATCH 513/818] The patch is the result of applying the upstream patch and running the maintainer scripts to regenerate the interface files. --- .../f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch | 1527 +++++++++++++++++ .../f/FFTW/FFTW-3.3.6-gompi-2017a.eb | 4 + .../f/FFTW/FFTW-3.3.6-intel-2017a.eb | 29 + 3 files changed, 1560 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch new file mode 100644 index 0000000000..70d5168fbf --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -0,0 +1,1527 @@ +# The scrips that generate the MPI F03 interface was broken in 3.3.6-pl1 +# The scripts were using fftw3.h from /usr/include, not ../api, and were +# failing silently if fftw3.h was not installed. This bug led to a +# fftw-3.3.6pl1 release with incomplete mpi/f03 header files. +# See commit 83092f8efbf872aefe7cfc6ee8fa43412f8e167a in FFTW upstream +# git. +# +# This patch is the result of applying that commit and running the +# maintainer mode scripts. +# +# Åke Sandgrem 2017-03-07 +diff -ru fftw-3.3.6-pl1.orig/mpi/f03api.sh fftw-3.3.6-pl1/mpi/f03api.sh +--- fftw-3.3.6-pl1.orig/mpi/f03api.sh 2017-01-15 13:03:24.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03api.sh 2017-03-08 15:46:56.000000002 +0100 +@@ -37,7 +37,7 @@ + + echo + echo " interface" +- grep -v 'mpi.h' fftw3-mpi.h | gcc -D__GNUC__=5 -D__i386__ -E - |grep "fftw${p}_mpi_init" |tr ';' '\n' | perl ../api/genf03.pl ++ grep -v 'mpi.h' fftw3-mpi.h | gcc -I../api -D__GNUC__=5 -D__i386__ -E - |grep "fftw${p}_mpi_init" |tr ';' '\n' | perl ../api/genf03.pl + echo " end interface" + + done +diff -ru fftw-3.3.6-pl1.orig/mpi/f03-wrap.c fftw-3.3.6-pl1/mpi/f03-wrap.c +--- fftw-3.3.6-pl1.orig/mpi/f03-wrap.c 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03-wrap.c 2017-03-08 16:20:11.000000002 +0100 +@@ -3,3 +3,282 @@ + #include "fftw3-mpi.h" + #include "ifftw-mpi.h" + ++FFTW_EXTERN ptrdiff_t XM(local_size_many_transposed_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_many_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_transposed_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_many_1d_f03)(ptrdiff_t n0, ptrdiff_t howmany, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_1d_f03)(ptrdiff_t n0, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_2d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_3d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN X(plan) XM(plan_many_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, R * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block, ptrdiff_t tblock, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_1d_f03)(ptrdiff_t n0, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_r2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_f03)(int rnk, const ptrdiff_t * n, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, X(r2r_kind) kind2, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_r2c_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_f03)(int rnk, const ptrdiff_t * n, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_c2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN void XM(gather_wisdom_f03)(MPI_Fint f_comm_); ++FFTW_EXTERN void XM(broadcast_wisdom_f03)(MPI_Fint f_comm_); ++ ++ptrdiff_t XM(local_size_many_transposed_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many_transposed)(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_many_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many)(rnk,n,howmany,block0,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_transposed_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_transposed)(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size)(rnk,n,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_many_1d_f03)(ptrdiff_t n0, ptrdiff_t howmany, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many_1d)(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start); ++} ++ ++ptrdiff_t XM(local_size_1d_f03)(ptrdiff_t n0, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_1d)(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start); ++} ++ ++ptrdiff_t XM(local_size_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_2d)(n0,n1,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_2d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_2d_transposed)(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_3d)(n0,n1,n2,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_3d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_3d_transposed)(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++X(plan) XM(plan_many_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, R * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_transpose)(n0,n1,howmany,block0,block1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_transpose)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_many_dft_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block, ptrdiff_t tblock, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft)(rnk,n,howmany,block,tblock,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft)(rnk,n,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_1d_f03)(ptrdiff_t n0, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_1d)(n0,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_2d)(n0,n1,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_3d)(n0,n1,n2,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_many_r2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_r2r)(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags); ++} ++ ++X(plan) XM(plan_r2r_f03)(int rnk, const ptrdiff_t * n, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r)(rnk,n,in,out,comm,kind,flags); ++} ++ ++X(plan) XM(plan_r2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r_2d)(n0,n1,in,out,comm,kind0,kind1,flags); ++} ++ ++X(plan) XM(plan_r2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, X(r2r_kind) kind2, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r_3d)(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags); ++} ++ ++X(plan) XM(plan_many_dft_r2c_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft_r2c)(rnk,n,howmany,iblock,oblock,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_f03)(int rnk, const ptrdiff_t * n, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c)(rnk,n,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c_2d)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c_3d)(n0,n1,n2,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_many_dft_c2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft_c2r)(rnk,n,howmany,iblock,oblock,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r)(rnk,n,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r_2d)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r_3d)(n0,n1,n2,in,out,comm,flags); ++} ++ ++void XM(gather_wisdom_f03)(MPI_Fint f_comm_) ++{ ++ MPI_Comm comm_; ++ ++ comm_ = MPI_Comm_f2c(f_comm_); ++ XM(gather_wisdom)(comm_); ++} ++ ++void XM(broadcast_wisdom_f03)(MPI_Fint f_comm_) ++{ ++ MPI_Comm comm_; ++ ++ comm_ = MPI_Comm_f2c(f_comm_); ++ XM(broadcast_wisdom)(comm_); ++} +diff -ru fftw-3.3.6-pl1.orig/mpi/f03-wrap.sh fftw-3.3.6-pl1/mpi/f03-wrap.sh +--- fftw-3.3.6-pl1.orig/mpi/f03-wrap.sh 2017-01-15 13:03:24.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03-wrap.sh 2017-03-08 15:46:56.000000002 +0100 +@@ -15,8 +15,8 @@ + echo + + # Declare prototypes using FFTW_EXTERN, important for Windows DLLs +-grep -v 'mpi.h' fftw3-mpi.h | gcc -E - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl | grep "MPI_Fint" | sed 's/^/FFTW_EXTERN /;s/$/;/' ++grep -v 'mpi.h' fftw3-mpi.h | gcc -E -I../api - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl | grep "MPI_Fint" | sed 's/^/FFTW_EXTERN /;s/$/;/' + +-grep -v 'mpi.h' fftw3-mpi.h | gcc -E - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl ++grep -v 'mpi.h' fftw3-mpi.h | gcc -E -I../api - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl + + +diff -ru fftw-3.3.6-pl1.orig/mpi/fftw3l-mpi.f03.in fftw-3.3.6-pl1/mpi/fftw3l-mpi.f03.in +--- fftw-3.3.6-pl1.orig/mpi/fftw3l-mpi.f03.in 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/fftw3l-mpi.f03.in 2017-03-08 16:20:11.000000002 +0100 +@@ -8,4 +8,398 @@ + end type fftwl_mpi_ddim + + interface ++ subroutine fftwl_mpi_init() bind(C, name='fftwl_mpi_init') ++ import ++ end subroutine fftwl_mpi_init ++ ++ subroutine fftwl_mpi_cleanup() bind(C, name='fftwl_mpi_cleanup') ++ import ++ end subroutine fftwl_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftwl_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftwl_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwl_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftwl_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwl_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftwl_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftwl_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_transpose ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft ++ ++ type(C_PTR) function fftwl_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftwl_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftwl_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftwl_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) & ++ bind(C, name='fftwl_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r_3d ++ ++ subroutine fftwl_mpi_gather_wisdom(comm_) bind(C, name='fftwl_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwl_mpi_gather_wisdom ++ ++ subroutine fftwl_mpi_broadcast_wisdom(comm_) bind(C, name='fftwl_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwl_mpi_broadcast_wisdom ++ ++ subroutine fftwl_mpi_execute_dft(p,in,out) bind(C, name='fftwl_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft ++ ++ subroutine fftwl_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftwl_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_LONG_DOUBLE), dimension(*), intent(inout) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft_r2c ++ ++ subroutine fftwl_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftwl_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft_c2r ++ ++ subroutine fftwl_mpi_execute_r2r(p,in,out) bind(C, name='fftwl_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_LONG_DOUBLE), dimension(*), intent(inout) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_r2r ++ + end interface +diff -ru fftw-3.3.6-pl1.orig/mpi/fftw3-mpi.f03.in fftw-3.3.6-pl1/mpi/fftw3-mpi.f03.in +--- fftw-3.3.6-pl1.orig/mpi/fftw3-mpi.f03.in 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/fftw3-mpi.f03.in 2017-03-08 16:20:11.000000002 +0100 +@@ -13,6 +13,399 @@ + end type fftw_mpi_ddim + + interface ++ subroutine fftw_mpi_init() bind(C, name='fftw_mpi_init') ++ import ++ end subroutine fftw_mpi_init ++ ++ subroutine fftw_mpi_cleanup() bind(C, name='fftw_mpi_cleanup') ++ import ++ end subroutine fftw_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftw_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftw_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftw_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftw_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftw_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftw_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftw_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_transpose ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft ++ ++ type(C_PTR) function fftw_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft ++ ++ type(C_PTR) function fftw_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftw_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftw_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftw_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r ++ ++ type(C_PTR) function fftw_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftw_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftw_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) bind(C, name='fftw_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r_3d ++ ++ subroutine fftw_mpi_gather_wisdom(comm_) bind(C, name='fftw_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftw_mpi_gather_wisdom ++ ++ subroutine fftw_mpi_broadcast_wisdom(comm_) bind(C, name='fftw_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftw_mpi_broadcast_wisdom ++ ++ subroutine fftw_mpi_execute_dft(p,in,out) bind(C, name='fftw_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft ++ ++ subroutine fftw_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftw_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_DOUBLE), dimension(*), intent(inout) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft_r2c ++ ++ subroutine fftw_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftw_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft_c2r ++ ++ subroutine fftw_mpi_execute_r2r(p,in,out) bind(C, name='fftw_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_DOUBLE), dimension(*), intent(inout) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_r2r ++ + end interface + + type, bind(C) :: fftwf_mpi_ddim +@@ -20,4 +413,398 @@ + end type fftwf_mpi_ddim + + interface ++ subroutine fftwf_mpi_init() bind(C, name='fftwf_mpi_init') ++ import ++ end subroutine fftwf_mpi_init ++ ++ subroutine fftwf_mpi_cleanup() bind(C, name='fftwf_mpi_cleanup') ++ import ++ end subroutine fftwf_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftwf_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftwf_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwf_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftwf_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwf_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftwf_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftwf_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_transpose ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft ++ ++ type(C_PTR) function fftwf_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftwf_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftwf_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftwf_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) & ++ bind(C, name='fftwf_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r_3d ++ ++ subroutine fftwf_mpi_gather_wisdom(comm_) bind(C, name='fftwf_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwf_mpi_gather_wisdom ++ ++ subroutine fftwf_mpi_broadcast_wisdom(comm_) bind(C, name='fftwf_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwf_mpi_broadcast_wisdom ++ ++ subroutine fftwf_mpi_execute_dft(p,in,out) bind(C, name='fftwf_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft ++ ++ subroutine fftwf_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftwf_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_FLOAT), dimension(*), intent(inout) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft_r2c ++ ++ subroutine fftwf_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftwf_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft_c2r ++ ++ subroutine fftwf_mpi_execute_r2r(p,in,out) bind(C, name='fftwf_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_FLOAT), dimension(*), intent(inout) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_r2r ++ + end interface diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 039c1bb824..4325e0c729 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -12,6 +12,10 @@ source_urls = [homepage] sources = ['fftw-%(version)s-pl1.tar.gz'] checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb new file mode 100644 index 0000000000..07c5fa9224 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -0,0 +1,29 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma +use_fma = False + +runtest = 'check' + +moduleclass = 'numlib' -- GitLab From 6f719a74f5ac27d67427c5cc6a1063745ced50ff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 09:08:33 +0200 Subject: [PATCH 514/818] Updated the patch with the URL to the upstream commit from fftw git. --- .../easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch index 70d5168fbf..f09a971da7 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -2,13 +2,15 @@ # The scripts were using fftw3.h from /usr/include, not ../api, and were # failing silently if fftw3.h was not installed. This bug led to a # fftw-3.3.6pl1 release with incomplete mpi/f03 header files. -# See commit 83092f8efbf872aefe7cfc6ee8fa43412f8e167a in FFTW upstream -# git. +# +# See commit +# https://github.com/FFTW/fftw3/commit/83092f8efbf872aefe7cfc6ee8fa43412f8e167a +# in FFTW upstream git. # # This patch is the result of applying that commit and running the # maintainer mode scripts. # -# Åke Sandgrem 2017-03-07 +# Åke Sandgren, 2017-03-07 diff -ru fftw-3.3.6-pl1.orig/mpi/f03api.sh fftw-3.3.6-pl1/mpi/f03api.sh --- fftw-3.3.6-pl1.orig/mpi/f03api.sh 2017-01-15 13:03:24.000000002 +0100 +++ fftw-3.3.6-pl1/mpi/f03api.sh 2017-03-08 15:46:56.000000002 +0100 -- GitLab From 4a0b7275c165adf41ab75b4d3fc1082f51388bb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:05:20 +0100 Subject: [PATCH 515/818] {tools}LSMS-3_rev237 --- easybuild/easyconfigs/l/LSMS-3_rev237.eb | 31 ++++++ easybuild/easyconfigs/l/LSMS-Makefiles.patch | 106 +++++++++++++++++++ 2 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSMS-3_rev237.eb create mode 100644 easybuild/easyconfigs/l/LSMS-Makefiles.patch diff --git a/easybuild/easyconfigs/l/LSMS-3_rev237.eb b/easybuild/easyconfigs/l/LSMS-3_rev237.eb new file mode 100644 index 0000000000..014f9beea4 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS-3_rev237.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'LSMS' +version = '3_rev237' + +homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' +description = "LSMS benchmark, part of CORAL suite" + +toolchain = {'name': 'foss', 'version': '2015g' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-Makefiles.patch'] + +files_to_copy = ['bin/lsms', 'bin/wl-lsms'] + +buildopts = '-j 1' + +dependencies = [ + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': ['lsms', 'wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS-Makefiles.patch new file mode 100644 index 0000000000..5c1f5e5908 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS-Makefiles.patch @@ -0,0 +1,106 @@ +--- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 ++++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 +@@ -1,6 +1,29 @@ + dlvl = ./. + include $(dlvl)/Makefile.in +-include ../architecture.h ++ ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + all: alllib alltst + +--- LSMS_3_rev237/src/Test/buildKKRMatrixTest/Makefile 2012-02-15 19:41:17.000000000 +0100 ++++ LSMS_3_rev237_working/src/Test/buildKKRMatrixTest/Makefile 2017-03-09 15:47:04.088863802 +0100 +@@ -3,7 +3,29 @@ + export INC_PATH = + export LIBS := + +-include $(TOP_DIR)/architecture.h ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + export INC_PATH += -I $(TOP_DIR)/include -I $(TOP_DIR)/src + export MISC = $(TOP_DIR)/src/Misc +--- LSMS_3_rev237/Makefile 2017-03-09 15:47:50.699882415 +0100 ++++ LSMS_3_rev237_working/Makefile 2017-03-09 14:58:44.845436772 +0100 +@@ -1,10 +1,35 @@ + + export TOP_DIR = $(shell pwd) +-export INC_PATH = + # export LIBS := -L$(TOP_DIR)/lua/lib -llua $(TOP_DIR)/mjson/mjson.a + export LIBS := $(TOP_DIR)/lua/lib/liblua.a $(TOP_DIR)/mjson/mjson.a + +-include architecture.h ++export CC = gcc ++export CXX = g++ ++export F77 = gfortran ++ ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + + all: liblua $(ADDITIONAL_TARGETS) libmjson LSMS -- GitLab From bc135bc82da4d927fa86526d64fac52b273fd338 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:15:58 +0100 Subject: [PATCH 516/818] change directory and added toolchain to name --- .../l/{LSMS-3_rev237.eb => LSMS/LSMS-3_rev237-foss-2015g.eb} | 0 easybuild/easyconfigs/l/{ => LSMS}/LSMS-Makefiles.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/{LSMS-3_rev237.eb => LSMS/LSMS-3_rev237-foss-2015g.eb} (100%) rename easybuild/easyconfigs/l/{ => LSMS}/LSMS-Makefiles.patch (100%) diff --git a/easybuild/easyconfigs/l/LSMS-3_rev237.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb similarity index 100% rename from easybuild/easyconfigs/l/LSMS-3_rev237.eb rename to easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb diff --git a/easybuild/easyconfigs/l/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch similarity index 100% rename from easybuild/easyconfigs/l/LSMS-Makefiles.patch rename to easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch -- GitLab From 12a958880fea5a3840959fada778f82ab132238f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:33:54 +0100 Subject: [PATCH 517/818] change $root to $root/bin --- .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb index 014f9beea4..c708bb19a4 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb @@ -15,17 +15,18 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +files_to_copy = ['bin'] buildopts = '-j 1' -dependencies = [ - ('HDF5', '1.8.16'), +dependencies = [ + ('HDF5', '1.8.16'), ] sanity_check_paths = { - 'files': ['lsms', 'wl-lsms'], + 'files': ['bin/lsms', 'bin/wl-lsms'], 'dirs': [], } - + moduleclass = 'tools' -- GitLab From 8fe97272f49beba4d341c2b087eac159294f9606 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:45:25 +0100 Subject: [PATCH 518/818] remove singularity --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb deleted file mode 100644 index e1e43de48b..0000000000 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Singularity' -version = '2.2.1' - -homepage = 'http://gmkurtzer.github.io/singularity' -description = """Singularity is a portable application stack packaging and runtime utility.""" - -toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} - -source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] -sources = ['%(version)s.tar.gz'] - -builddependencies = [('Autotools', '20150215')] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], - 'dirs': ['etc', 'libexec/singularity'], -} - -moduleclass = 'tools' -- GitLab From c4732f5b681ee9ec959c2bf50470ff9c6b24704a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:09:46 +0100 Subject: [PATCH 519/818] add LSMS-3_rev237-foss-2016a --- .../l/LSMS/LSMS-3_rev237-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb new file mode 100644 index 0000000000..ff6c8b7de3 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'LSMS' +version = '3_rev237' + +homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' +description = "LSMS benchmark, part of CORAL suite" + +toolchain = {'name': 'foss', 'version': '2016a' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-Makefiles.patch'] + +#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +files_to_copy = ['bin'] + +buildopts = '-j 1' + +dependencies = [ + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': ['bin/lsms', 'bin/wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a05f85ff643946fe8058d7a839a979093f2b7239 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 11:31:59 +0200 Subject: [PATCH 520/818] adding easyconfigs: arpack-ng-3.4.0-foss-2017a.eb, arpack-ng-3.4.0-intel-2017a.eb --- .../a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb | 25 +++++++++++++++++++ .../arpack-ng/arpack-ng-3.4.0-intel-2017a.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb new file mode 100644 index 0000000000..12081625ca --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb new file mode 100644 index 0000000000..f92abdeafa --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 587c000e0c2e3dfc7f6e6c6f03713a725841813f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:35:36 +0100 Subject: [PATCH 521/818] remove #... comment --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb | 1 - easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb index c708bb19a4..34bdeac5c9 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb @@ -15,7 +15,6 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] files_to_copy = ['bin'] buildopts = '-j 1' diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index ff6c8b7de3..fa65d19eb5 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -15,7 +15,6 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] files_to_copy = ['bin'] buildopts = '-j 1' -- GitLab From 91015b03a8a9dd192e46e16e20c22a47a8d55c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:46:11 +0100 Subject: [PATCH 522/818] remove eb for LSMS-3_rev237-foss-2015g.eb --- .../l/LSMS/LSMS-3_rev237-foss-2015g.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb deleted file mode 100644 index 34bdeac5c9..0000000000 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'MakeCp' - -name = 'LSMS' -version = '3_rev237' - -homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' -description = "LSMS benchmark, part of CORAL suite" - -toolchain = {'name': 'foss', 'version': '2015g' } - -source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] -sources = ['%(name)s_%(version)s.tar.bz2'] - -checksums = ['8c864c9223b93488663815557e61cd0b'] - -patches = ['LSMS-Makefiles.patch'] - -files_to_copy = ['bin'] - -buildopts = '-j 1' - -dependencies = [ - ('HDF5', '1.8.16'), -] - -sanity_check_paths = { - 'files': ['bin/lsms', 'bin/wl-lsms'], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From 8b8979ea29dd134984613cb79ebbb6e54216e1f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 10:50:16 +0100 Subject: [PATCH 523/818] adding easyconfigs: SWASH-4.01-intel-2017a-mpi.eb --- .../s/SWASH/SWASH-4.01-intel-2017a-mpi.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb new file mode 100644 index 0000000000..57c47cdddd --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '4.01' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' -- GitLab From 5129611740578748995df814108c604e645b9f98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 10:56:56 +0100 Subject: [PATCH 524/818] fixed homepage and source_urls --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 759ecb7840..3da591ce62 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.0.7' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index f0b4020253..d13e7d8912 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.0.7' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] patches = ['ViennaRNA_ictce-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 106d2f71e3..3e54d3ed83 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.1.6' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_1_x/'] patches = ['ViennaRNA-2.1.6_ictce.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 714f3edc9e..1988a82b1e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.2.3' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_2_x/'] patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] -- GitLab From 773a85389fae914ab1520ec122b738c621bc8cd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 10:57:22 +0100 Subject: [PATCH 525/818] added ViennaRNA-2.3.4-foss-2016b --- .../v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb new file mode 100644 index 0000000000..5b2bac1762 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.3.4' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/'] + +checksums = ['c77bff267606d22557a4f867df635822'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a3afeb3f7dcda784d5a8e79ebb8a7365edf912f9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 12:22:05 +0200 Subject: [PATCH 526/818] Use SHLIB_EXT instead of hardcoded ".so" --- easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb index 12081625ca..f7c3095a50 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb @@ -18,7 +18,7 @@ preconfigopts = "sh bootstrap && " configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb index f92abdeafa..17c7254907 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb @@ -18,7 +18,7 @@ preconfigopts = "sh bootstrap && " configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], 'dirs': [] } -- GitLab From 6760a85f0f6e38d783af94b074b4c2d684bf579b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:22:55 +0100 Subject: [PATCH 527/818] pass $FFLAGS to $FLAGS_OPT for SWASH --- easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb index 57c47cdddd..58632f03e4 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 -- GitLab From 7ed9150a0c5b3a194039f14ba74a46484abe55dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:57:00 +0100 Subject: [PATCH 528/818] {lib}[intel/2016b] Tensorflow v1.0.1 w/ Python 2.7.12 + 3.5.2 --- ...sorflow-1.0.1-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ ...nsorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..f1c3f15e89 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/7e/7c/f398393beab1647be0a5e6974b8a34e4ea2d3cb7bd9e38bd43a657ed27d1/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['5c88e656fcd34cd89d4cf48d3ec7dd67'] + +dependencies = [ + ('Python', '%s.%s.12' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..2d9a2afe66 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '3' +pymin = '5' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['bccff4d9b87331d4dcecafa43c970b89'] + +dependencies = [ + ('Python', '%s.%s.2' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From fe7e8ddf7a2583411547d522ce9b297a07bc9cb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:59:35 +0100 Subject: [PATCH 529/818] fix sources spec for Tensorflow 1.0.1 w/ Python 3.5.2 --- .../t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb index 2d9a2afe66..42b703619c 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -15,7 +15,7 @@ pymajmin = pymaj + pymin source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] sources = [ - 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] checksums = ['bccff4d9b87331d4dcecafa43c970b89'] -- GitLab From 689d70e53f565ae1b0a6a5917182b633f72be48a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 13:24:33 +0100 Subject: [PATCH 530/818] pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs --- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb index 767e04327d..c01885134c 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb index a9d434ebd1..b19bb39b27 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'omp' +buildopts = 'omp FLAGS_OPT="$FFLAGS"' parallel = 1 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb index ad04f26f31..1ff3f68105 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb @@ -14,7 +14,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'ser' +buildopts = 'ser FLAGS_OPT="$FFLAGS"' parallel = 1 -- GitLab From d12d27667f6a522666539d2d5a0e44993c18b7d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 13:47:47 +0100 Subject: [PATCH 531/818] adding easyconfigs: ImageJ-1.51k.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb new file mode 100644 index 0000000000..ec975dfc22 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -0,0 +1,40 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.51k' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'https://imagej.nih.gov/ij/download/src/', + 'http://www.mecourse.com/landinig/software/', +] +sources = [ + 'ij%(version_major)s%(version_minor)s-src.zip', + 'morphology.zip', +] +checksums = [ + 'e7b634bd1d46cec7694a6990180c5cd9', # ij151k-src.zip + '21491b55bbef5cc50ebff495a4d2b420', # morphology.zip +] + +dependencies = [ + ('Java', '1.8.0_121'), +] + +builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] + +install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " +install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dplugins.dir=$EBROOTIMAGE/plugins'\n" + +moduleclass = 'tools' -- GitLab From a57f5ac9fda2e860342fcd32051027934120b5a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 14:04:35 +0100 Subject: [PATCH 532/818] correctly specify location of plugins for ImageJ --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb index ec975dfc22..9875b136f1 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -35,6 +35,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dplugins.dir=$EBROOTIMAGE/plugins'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGE/plugins'\n" moduleclass = 'tools' -- GitLab From 50d330cc3ae39f3ef14a287c0e92ffa9d7782cd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 14:09:10 +0100 Subject: [PATCH 533/818] add easyconfigs for ant/JUnit build deps for ImageJ 1.51k --- .../a/ant/ant-1.10.1-Java-1.8.0_121.eb | 26 +++++++++++++++++++ .../j/JUnit/JUnit-4.12-Java-1.8.0_121.eb | 22 ++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb new file mode 100644 index 0000000000..42ed3e6196 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.10.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_121')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb new file mode 100644 index 0000000000..43aa70ed7b --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_121')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a22fd2b0ff22c524c032bbe7974ef910699cb6bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:02:55 +0100 Subject: [PATCH 534/818] @boegel LSMS-3_rev237-foss-2016a.eb - buildopts = '-j 1' -> parallel = 1 && move dependencies, below patches --- .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index fa65d19eb5..3ca77887d0 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -15,13 +15,13 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -files_to_copy = ['bin'] +dependencies = [ + ('HDF5', '1.8.16'), +] -buildopts = '-j 1' +files_to_copy = ['bin'] -dependencies = [ - ('HDF5', '1.8.16'), -] +parallel = 1 sanity_check_paths = { 'files': ['bin/lsms', 'bin/wl-lsms'], -- GitLab From 9c29e8517e77273ba61625703c06025da2dcb73b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:06:38 +0100 Subject: [PATCH 535/818] {tools}LSMS-3_rev237 renamed LSMS-Makefiles.patch -> LSMS-3_rev237_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 2 +- .../{LSMS-Makefiles.patch => LSMS-3_rev237_fix-Makefiles.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/LSMS/{LSMS-Makefiles.patch => LSMS-3_rev237_fix-Makefiles.patch} (100%) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index 3ca77887d0..198945fde4 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(name)s_%(version)s.tar.bz2'] checksums = ['8c864c9223b93488663815557e61cd0b'] -patches = ['LSMS-Makefiles.patch'] +patches = ['LSMS-3_rev237_fix-Makefiles.patch'] dependencies = [ ('HDF5', '1.8.16'), diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch similarity index 100% rename from easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch rename to easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch -- GitLab From d3026219c7e50a7fa5e18488b33dd77711ffb30f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:18:43 +0100 Subject: [PATCH 536/818] {tools}LSMS-3_rev237 add head LSMS-3_rev237_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch index 5c1f5e5908..e650269d91 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -1,3 +1,5 @@ +#change PATH and exports +#Golasowski Martin, martin.golasowski@vsb.cz, 2016 IT4Innovations --- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 +++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 @@ -1,6 +1,29 @@ -- GitLab From 31b9523262215334f596cde4ac75aae9242e2798 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:25:21 +0100 Subject: [PATCH 537/818] {tools}LSMS-3_rev237 2016 -> 2017 --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch index e650269d91..191092dc63 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -1,5 +1,5 @@ #change PATH and exports -#Golasowski Martin, martin.golasowski@vsb.cz, 2016 IT4Innovations +#Golasowski Martin, martin.golasowski@vsb.cz, 2017 IT4Innovations --- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 +++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 @@ -1,6 +1,29 @@ -- GitLab From a1bc03948dde0ab43e356d72a91f8d543f6c4202 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 15:32:02 +0100 Subject: [PATCH 538/818] changed source_urls to use templates --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 3da591ce62..45a8cbb1a5 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index d13e7d8912..fafae9335e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA_ictce-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 3e54d3ed83..29c51c1030 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_1_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA-2.1.6_ictce.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 1988a82b1e..3214395e25 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_2_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb index 5b2bac1762..ec625ff6c6 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] checksums = ['c77bff267606d22557a4f867df635822'] -- GitLab From 7a01868d8490d06d2ef9786713232c44550a0cb6 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 13 Mar 2017 17:19:43 +0100 Subject: [PATCH 539/818] HDF5 1.10.0 patch1 for golfs incl. dependencies This is a simple port from foss/2016b - same gcc compiler --- .../HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb | 22 ++++++++++++++++++ .../s/Szip/Szip-2.1-goolfc-2016.10.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb new file mode 100644 index 0000000000..a728a33f56 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb new file mode 100644 index 0000000000..c2c5a38e56 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 774f17a8c7232229bdf1d3520a30a1608c94fda3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Tue, 14 Mar 2017 07:33:04 +0100 Subject: [PATCH 540/818] {tools}LSMS-3_rev237 change LSMS-3_rev237_fix-Makefiles.patch -> LSMS-%(version)s_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index 198945fde4..b39dd8a48b 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(name)s_%(version)s.tar.bz2'] checksums = ['8c864c9223b93488663815557e61cd0b'] -patches = ['LSMS-3_rev237_fix-Makefiles.patch'] +patches = ['LSMS-%(version)s_fix-Makefiles.patch'] dependencies = [ ('HDF5', '1.8.16'), -- GitLab From 152c3f7593cef4db3a1197f42adef4734a8c12a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2017 15:20:50 +0100 Subject: [PATCH 541/818] remove unneeded CMake easyconfig --- .../c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb deleted file mode 100644 index 50e2df64aa..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.6.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'GCCcore', 'version': '6.3.0'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -builddependencies = [ - ('binutils', '2.27'), -] - - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 40f76e4b2f7d9e80850d6b94f5dfdec20bf15c99 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Mar 2017 16:21:25 +0200 Subject: [PATCH 542/818] adding easyconfigs: GROMACS-2016.3-foss-2017a.eb --- .../g/GROMACS/GROMACS-2016.3-foss-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb new file mode 100644 index 0000000000..c3f26a2915 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' -- GitLab From 3d561c8d11759dda93628cbd5ddea9f294e1537c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2017 16:30:25 +0100 Subject: [PATCH 543/818] adding easyconfigs: GROMACS-2016.3-intel-2017a.eb --- .../g/GROMACS/GROMACS-2016.3-intel-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb new file mode 100644 index 0000000000..edcd456df0 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' -- GitLab From 13d0854b39af72736c182706b19fb7ee83ddcec8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 14 Mar 2017 18:32:41 +0000 Subject: [PATCH 544/818] Updated PETSc recipe to the modified version of the download install feature. --- .../PETSc/PETSc-3.7.5-intel-2016a-download.eb | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb index a59522d52f..111a8d2edd 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb @@ -1,5 +1,6 @@ name = 'PETSc' version = '3.7.5' +versionsuffix = '-downloaded_deps' homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -11,31 +12,32 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [('CMake', '3.5.2')] shared_libs = 1 pic = 1 downloadinstall = True +# For these dependencies, we do not download them dependencies = [('HDF5','1.8.18')] - configopts = "" -# compiles PETSc shared configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" -# external packages that are downloaded -external_packages = ['mumps', 'ptscotch', 'superlu', 'superlu_dist', 'parmetis', 'metis', 'ml', 'suitesparse', 'hypre', 'prometheus'] -# compiles the external dependencies non-shared -external_packages_shared = "no" -for p in external_packages: - configopts += "--download-%s=yes --download-%s-shared=%s " % (p,p,external_packages_shared) -configopts += "--download-triangle=yes" # download-triangle-shared is not supported - -builddependencies = [('CMake', '3.5.2')] +# external packages that are downloaded with --download-=1 and --download--static=1 +download_deps_static = [ + 'hypre', + 'metis', + 'ml', + 'mumps', + 'parmetis', + 'prometheus', + 'ptscotch', + 'suitesparse', + 'superlu', + 'superlu_dist' +] +# triangle cannot be downloaded with --download-triangle-static because it fails +download_deps = ['triangle'] moduleclass = 'numlib' - -modluafooter = """ -family("petsc") -""" - -- GitLab From 11c424082a6f064552f34bc0e74a766cebbbd695 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:25:33 +0100 Subject: [PATCH 545/818] Add kaiju/1.5.0 --- .../k/Kaiju/kaiju-1.5.0-intel-2016b.eb | 27 ++++++++++++++++ .../k/Kaiju/kaiju-1.5.0-makefile.patch | 31 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb new file mode 100644 index 0000000000..1a3e1acaed --- /dev/null +++ b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'Kaiju' +version = '1.5.0' + +homepage = 'http://kaiju.binf.ku.dk/' +description = """Kaiju is a program for sensitive taxonomic classification of high-throughput +sequencing reads from metagenomic whole genome sequencing experiments""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/bioinformatics-centre/kaiju/archive/'] + +patches = ['kaiju-%(version)s-makefile.patch'] + +start_dir = 'src' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['kaiju', 'kaiju2krona', 'kaijup', 'kaijuReport', 'kaijux']], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch new file mode 100644 index 0000000000..3ae20a25b6 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch @@ -0,0 +1,31 @@ +diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile +--- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 ++++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 +@@ -1,7 +1,7 @@ +-CC = gcc ++CC ?= gcc + #CFLAGS = -g +-CFLAGS = -O3 -g -Wno-unused-result +-LDLIBS = -lpthread -lm ++CFLAGS ?= -O3 -g -Wno-unused-result ++LDLIBS ?= -lpthread -lm + + all: mkbwt mkfmi Makefile + +diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +--- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 ++++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 +@@ -1,8 +1,8 @@ +-CC = gcc +-CXX = g++ +-CFLAGS = -g -O3 -DNDEBUG -Wall -Wno-uninitialized +-CXXFLAGS = -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +-LDLIBS = -lpthread ++CC ?= gcc ++CXX ?= g++ ++CFLAGS ?= -g -O3 -DNDEBUG -Wall -Wno-uninitialized ++CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function ++LDLIBS ?= -lpthread + INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ + + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From 1042b8e7ef4cf2bd8866e1ab43a2d8b3ecd918f4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:35:58 +0100 Subject: [PATCH 546/818] Use capitals for easyconfig file --- .../{kaiju-1.5.0-intel-2016b.eb => Kaiju-1.5.0-intel-2016b.eb} | 0 .../{kaiju-1.5.0-makefile.patch => Kaiju-1.5.0-makefile.patch} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/k/Kaiju/{kaiju-1.5.0-intel-2016b.eb => Kaiju-1.5.0-intel-2016b.eb} (100%) rename easybuild/easyconfigs/k/Kaiju/{kaiju-1.5.0-makefile.patch => Kaiju-1.5.0-makefile.patch} (100%) diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb rename to easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch similarity index 100% rename from easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch rename to easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch -- GitLab From 868ea7d2d5d5be6bdef3d33e8a91b89e1c230127 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:45:23 +0100 Subject: [PATCH 547/818] Fix name of patch --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb index 1a3e1acaed..7f4e002400 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb @@ -13,7 +13,7 @@ toolchainopts = {'cstd': 'c++11'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/bioinformatics-centre/kaiju/archive/'] -patches = ['kaiju-%(version)s-makefile.patch'] +patches = ['%(name)s-%(version)s-makefile.patch'] start_dir = 'src' -- GitLab From 765acc339dc67081c2630070b3f5c726609a375f Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 16 Mar 2017 09:32:27 +0100 Subject: [PATCH 548/818] Fixed wrong sanity check in Mesa --- .../m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 5 ++--- .../m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 5 ++--- .../m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 7 +++---- .../m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 7 +++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 10 ++++++---- 14 files changed, 79 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 41d6a64d37..d8ac10c171 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -64,9 +64,8 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/wmesa.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 8b03ae9140..d3f8230305 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -64,9 +64,8 @@ sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/wmesa.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 5224023e11..7d75f18d6f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -64,10 +64,9 @@ sanity_check_paths = { 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GLES/gl.h', 'include/GLES2/gl2.h', - 'include/GLES3/gl3.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index ec21cce29c..346166fe00 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -64,10 +64,9 @@ sanity_check_paths = { 'lib/libGLESv1_CM.so', 'lib/libGLESv2.so', 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GLES/gl.h', 'include/GLES2/gl2.h', - 'include/GLES3/gl3.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index 81337fce92..9b02d2b02b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 84db881b8b..45545e7c83 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 9a2892bda4..92703769fd 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index 8fe85b43fb..61b180d1ef 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index c0ae4f1fc2..6660454e4c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb index b8a0ae2d3f..8376070490 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -49,10 +49,13 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --di configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index d9578ef42b..2ac60cb5d0 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -49,10 +49,13 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --di configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index ea99e518c2..a2555dbfc0 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -47,10 +47,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', - 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'include/GL/wmesa.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 55c990890f..1ef5829725 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -48,10 +48,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', - 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'include/GL/wmesa.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 4b5ad07db8..6f68f37b53 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -48,10 +48,12 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], 'dirs': [] } -- GitLab From 2234ef0dd76e1809483f978a790f39731dc593c7 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 16 Mar 2017 10:02:28 +0100 Subject: [PATCH 549/818] Fixed a character introduced by mistake --- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index d8ac10c171..8757076334 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -65,7 +65,7 @@ sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], + 'include/GL/glx_mangle.h', 'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index d3f8230305..ffc67154d8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -65,7 +65,7 @@ sanity_check_paths = { 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], + 'include/GL/glx_mangle.h', 'include/GL/wmesa.h'], 'dirs': [] } -- GitLab From e782dc8c1ec30ea348a225a9fa1dc9ce8d7651f5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 16 Mar 2017 11:35:45 +0100 Subject: [PATCH 550/818] Explain what patch does --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch index 3ae20a25b6..94fd3d70c6 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch @@ -1,3 +1,5 @@ +# Let the makefiles use EB provides values if they are set +# wpoely86@gmail.com diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile --- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 @@ -9,9 +11,9 @@ diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile -LDLIBS = -lpthread -lm +CFLAGS ?= -O3 -g -Wno-unused-result +LDLIBS ?= -lpthread -lm - + all: mkbwt mkfmi Makefile - + diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile --- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 @@ -27,5 +29,5 @@ diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +LDLIBS ?= -lpthread INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ - + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From aa621c0d62036c47acd1ef0843033cc6e8f532f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 16 Mar 2017 11:44:38 +0100 Subject: [PATCH 551/818] Fix patch again (dropped whitespace) --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch index 94fd3d70c6..3ae20a25b6 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch @@ -1,5 +1,3 @@ -# Let the makefiles use EB provides values if they are set -# wpoely86@gmail.com diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile --- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 @@ -11,9 +9,9 @@ diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile -LDLIBS = -lpthread -lm +CFLAGS ?= -O3 -g -Wno-unused-result +LDLIBS ?= -lpthread -lm - + all: mkbwt mkfmi Makefile - + diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile --- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 @@ -29,5 +27,5 @@ diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +LDLIBS ?= -lpthread INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ - + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From 7db1bd4556ffbe3ed7aa2e128be29cb1016da9b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Mar 2017 12:26:50 +0100 Subject: [PATCH 552/818] adding easyconfigs: MyMediaLite-3.12-intel-2017a.eb, Mono-4.8.0.495-intel-2017a.eb --- .../m/Mono/Mono-4.8.0.495-intel-2017a.eb | 21 +++++++++++++++++++ .../MyMediaLite-3.12-intel-2017a.eb | 14 +++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb create mode 100644 easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb b/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb new file mode 100644 index 0000000000..7b8956bcd6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'Mono' +version = '4.8.0.495' + +homepage = 'http://www.mono-project.com/' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('Autotools', '20150215'), + ('CMake', '3.7.2'), + ('gettext', '0.19.8.1'), +] + +configopts = "--with-large-heap=yes --without-x" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb new file mode 100644 index 0000000000..63966d2c9c --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.12' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/zenogantner/MyMediaLite/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('Mono', '4.8.0.495')] + +moduleclass = 'lib' -- GitLab From 1c713b31d319cec1b07ac27b14befb58054f2b04 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Thu, 16 Mar 2017 16:39:42 +0100 Subject: [PATCH 553/818] SAMtools 1.4 - 2 additional dependencies (additional compression algorithms), but also needs a modified easyblock as errmod.h and kprobaln.h are no loger provided nor needed. --- .../s/SAMtools/SAMtools-1.4-intel-2016b.eb | 40 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.4_Makefile.patch | 21 ++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb new file mode 100644 index 0000000000..28fabf7d41 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-%(version)s_Makefile.patch'] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch new file mode 100644 index 0000000000..321f1c822c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch @@ -0,0 +1,21 @@ +# Use EB modules for zlib and ncurses +# Author: Kurt Lust, UAntwerpen +# Developed from the 1.3.1 patch by Adam Huffman of The Francis Crick Institute +--- samtools-1.4-orig/Makefile 2017-03-16 15:11:35.236460000 +0100 ++++ samtools-1.4/Makefile 2017-03-16 15:14:45.964895969 +0100 +@@ -86,13 +86,13 @@ + + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz $(LIBS) ++ALL_LIBS = -L$(EBROOTZLIB) -lz $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ -- GitLab From bb9402e3934ef52a1cfa253c9eddae1cbff90600 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 17 Mar 2017 08:41:47 +0100 Subject: [PATCH 554/818] {lang}[foss/2016b] R/3.3.3 w/ X11-20160819 (REVIEW) --- easybuild/easyconfigs/r/R/Cairo-1.5-9.patch | 33 ++ .../r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 509 ++++++++++++++++++ 2 files changed, 542 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/Cairo-1.5-9.patch create mode 100644 easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb diff --git a/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch b/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch new file mode 100644 index 0000000000..e88f9455e6 --- /dev/null +++ b/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch @@ -0,0 +1,33 @@ +# pkg-config --libs cairo-pdf +# and +# pkg-config --libs cairo-ps +# should return zlib library location, otherwise configure would use system zlib for cairo compilation tests +# (but not for the builds) +# in the cairo-{ps,pdf} +# Requires: cairo +# sould be +# Reuires: cairo zlib +# So It might be a cairo/pkg-config issue +# March 16th 2017 by B. Hajgato (Free Univeristy Brussels - VUB) +--- Cairo/MD5.org 2015-09-26 09:05:40.000000000 +0200 ++++ Cairo/MD5 2017-03-16 20:28:51.181957519 +0100 +@@ -4,7 +4,7 @@ + 652a130cdb89035bd21add505f09ff6c *R/Cairo.R + 45f780dde83799bfd5ec2d67659fded4 *R/imgtools.R + a9008f9a9abd726e834484d834008b47 *R/zzz.R +-c5196eb2ad5615b9198965124fbbc2f7 *configure ++0eb0d0ae1f7558f449dc797d3e37677d *configure + 938f465e81a73126bac6eabfdfce8ea0 *configure.ac + 9ab259fe324885b6524858aa98ab51ef *configure.win + 9b9c0bd04bd4f6444182d8a4b8e209b5 *man/Cairo.Rd +--- Cairo/configure.org 2015-09-25 19:49:11.000000000 +0200 ++++ Cairo/configure 2017-03-16 20:25:42.687704125 +0100 +@@ -3479,7 +3479,7 @@ + { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${modlist}" >&5 + $as_echo "${modlist}" >&6; } + CAIRO_CFLAGS=`"${PKGCONF}" --cflags ${modlist}` +- CAIRO_LIBS=`"${PKGCONF}" --libs ${modlist}` ++ CAIRO_LIBS="-L$EBROOTZLIB/lib `"${PKGCONF}" --libs ${modlist}`" + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb new file mode 100644 index 0000000000..2584758870 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -0,0 +1,509 @@ +name = 'R' +version = '3.3.3' +x11ver = '20160819' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.6'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), + ('PCRE', '8.39'), + ('libpng', '1.6.24'), # for plotting in R + ('libjpeg-turbo', '1.5.0'), # for plottting in R + ('LibTIFF', '4.0.6'), + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.5'), # for tcltk + ('Tk', '8.6.5'), # for tcltk + ('cURL', '7.49.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.0'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.1'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on March 7th 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-6', ext_options), + ('abind', '1.4-5', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.1', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.4', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-10', ext_options), + ('mclust', '5.2.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-5', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.0.5', ext_options), + ('checkmate', '1.8.2', ext_options), + ('Rcpp', '0.12.9', ext_options), + ('cubature', '1.3-6', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.1', 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'1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.1.1', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('imager', '0.31', ext_options), +] + +moduleclass = 'lang' + -- GitLab From 80146673bc89daf3861e7df57114c0aa32a68f23 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Fri, 17 Mar 2017 10:03:41 +0100 Subject: [PATCH 555/818] Removed unnecessary patch from SAMtools 1.4 and 1.3.1 for intel/2016b and removed the 1.4 patch file from the repository. --- .../s/SAMtools/SAMtools-1.3.1-intel-2016b.eb | 3 --- .../s/SAMtools/SAMtools-1.4-intel-2016b.eb | 3 --- .../s/SAMtools/SAMtools-1.4_Makefile.patch | 21 ------------------- 3 files changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb index 068f81d41a..ad73efb9d9 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb @@ -22,9 +22,6 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -# Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-%(version)s_Makefile.patch'] - dependencies = [ ('ncurses', '6.0'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index 28fabf7d41..3167310f24 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -25,9 +25,6 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -# Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-%(version)s_Makefile.patch'] - # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. dependencies = [ diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch deleted file mode 100644 index 321f1c822c..0000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch +++ /dev/null @@ -1,21 +0,0 @@ -# Use EB modules for zlib and ncurses -# Author: Kurt Lust, UAntwerpen -# Developed from the 1.3.1 patch by Adam Huffman of The Francis Crick Institute ---- samtools-1.4-orig/Makefile 2017-03-16 15:11:35.236460000 +0100 -+++ samtools-1.4/Makefile 2017-03-16 15:14:45.964895969 +0100 -@@ -86,13 +86,13 @@ - - ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz $(LIBS) -+ALL_LIBS = -L$(EBROOTZLIB) -lz $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. - - config.mk: -- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ -+ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ - - config.h: - echo '/* Basic config.h generated by Makefile */' > $@ -- GitLab From e96b2fbf0f49b0f448e32e7029def139d9143e3a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 17 Mar 2017 17:38:10 +0800 Subject: [PATCH 556/818] prepare release notes for eb312 --- RELEASE_NOTES | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 96a76caa5a..a515a07590 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,36 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.2 (March 17th 2017) +------------------------ + +bugfix release +- added example easyconfig files for 12 new software packages: + - DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335), + L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307), QJson (#4305), + QScintilla (#4306, #4313) +- added additional easyconfigs for various supported software packages, including: + - BLAT v3.5, FFTW v3.3.6, flex v2.6.3, FreeXL v1.0.2, GDAL v2.1.3, GEOS v3.6.1, GROMACS v2016.2 + v2016.3, + HDF5 1.10.0-patch1, help2man v1.47.4, ImageJ v1.51k, libspatialindex v1.8.5, libspatialite v4.3.0a, M4 v1.4.18, + Mono v4.8.0.495, MyMediaLite v3.12, PGI v17.1, PROJ v4.9.3, PyQt v4.12, QCA v2.1.3, QwtPolar v1.1.1, Qwt v6.1.3, + requests v2.13.0, SIP v4.19, SPAdes v3.10.1, STAR v2.5.2b, SWASH v4.01, SWIG v3.0.11, Tensorflow v1.0.1, + ViennaRNA 2.3.4, Yasm v1.3.0 +- various enhancements, including: + - fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318) + - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) +- various bug fixes, including: + - fix missing PYTHONPATH in ROOT v6.08.02 easyconfig (#4239) + - correct libjpeg turbo references in GDAL (#4276) + - fix to be sure the HDF5 provided by easybuild is used in BLASR (#4278) + - miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... (#4291) + - fix shebang in miRDeep2 Perl scripts (#4301) + - also check with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - also copy Rfam_for_miRDeep.fa to mirDeep2 directory (#4316) + - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) + - correctly set $PYTHONPATH in ROOT easyconfigs (#4331) + - add requests and psycopg2 as dependencies for QGIS (#4332) + + v3.1.1 (March 7th 2017) ----------------------- -- GitLab From e3cb8e7f412614e49f061056d460adc144640bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 13:28:43 +0100 Subject: [PATCH 557/818] adding easyconfigs: sketchmap-20170130-intel-2016b.eb --- .../sketchmap-20170130-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb b/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb new file mode 100644 index 0000000000..6caab74f6e --- /dev/null +++ b/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'sketchmap' +version = '20170130' +commit = '7e059bd' + +homepage = 'http://sketchmap.org/' +description = """Sketch-map is a dimensionality reduction algorithm that is particularly well suited to examining + the high-dimensionality data that is routinely produced in atomistic simulations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/cosmo-epfl/sketchmap/archive/'] +sources = ['%s.tar.gz' % commit] + +buildopts = 'CXX="$CXX" MAKEDEPEND="$CXX -M \$(CXXFLAGS)" LLAPACK="$LIBLAPACK_MT"' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/dimdist', 'bin/dimlandmark', 'bin/dimproj', 'bin/dimred'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From b886e0f5e7426e7fdb73dc73aa4eba4d96d134b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:25:31 +0100 Subject: [PATCH 558/818] adding easyconfigs: snaphu-1.4.2-intel-2016b.eb --- .../s/snaphu/snaphu-1.4.2-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb new file mode 100644 index 0000000000..8397d4ea59 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' -- GitLab From 5f80281a8224f78bc2f8b8544cb8fcb596f9b9ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:25:51 +0100 Subject: [PATCH 559/818] adding easyconfigs: Triangle-1.6-intel-2016b.eb --- .../t/Triangle/Triangle-1.6-intel-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb new file mode 100644 index 0000000000..f3df6e7173 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +dependencies = [ + ('X11', '20160819'), +] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 89a2a4661e0639138aef33016134925343aedb1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:32:46 +0100 Subject: [PATCH 560/818] remove unneeded X11 dep in Triangle easyconfig since 'showme' binary isn't being built --- easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb index f3df6e7173..77785bc785 100644 --- a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb @@ -18,10 +18,6 @@ checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] patches = ['%(name)s-%(version)s_makefile.patch'] -dependencies = [ - ('X11', '20160819'), -] - buildopts = 'triangle trilibrary' files_to_copy = [ -- GitLab From a10c62c9e46d52fa47d1eae69f094c52307c559b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 18 Mar 2017 09:33:54 +0100 Subject: [PATCH 561/818] adding easyconfigs: SAMtools-1.4-foss-2016b.eb --- .../s/SAMtools/SAMtools-1.4-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb new file mode 100644 index 0000000000..340f9547b8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 491b626efb646f6115990fb080b7267d23737efe Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 18 Mar 2017 10:06:18 +0100 Subject: [PATCH 562/818] adding easyconfigs: HTSlib-1.4-foss-2016b.eb, HTSlib-1.4-intel-2016b.eb --- .../h/HTSlib/HTSlib-1.4-foss-2016b.eb | 36 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.4-intel-2016b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb new file mode 100644 index 0000000000..9bdb215d4c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb new file mode 100644 index 0000000000..5c5a91710c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3e057c110297155dcb957faa7a10335bdc21613b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2017 11:07:56 +0100 Subject: [PATCH 563/818] complete release notes for EasyBuild v3.1.2 & bump version --- RELEASE_NOTES | 40 ++++++++++++++++++---------------------- setup.py | 2 +- 2 files changed, 19 insertions(+), 23 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a515a07590..1faff06d0d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,43 +3,39 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, +The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.2 (March 17th 2017) +v3.1.2 (March 20th 2017) ------------------------ -bugfix release -- added example easyconfig files for 12 new software packages: +bugfix/update release +- add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (#4334) + - note that this warrants rebuilding FFTW that is a part of foss/2017a +- added example easyconfig files for 14 new software packages: - DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335), - L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307), QJson (#4305), - QScintilla (#4306, #4313) -- added additional easyconfigs for various supported software packages, including: - - BLAT v3.5, FFTW v3.3.6, flex v2.6.3, FreeXL v1.0.2, GDAL v2.1.3, GEOS v3.6.1, GROMACS v2016.2 + v2016.3, - HDF5 1.10.0-patch1, help2man v1.47.4, ImageJ v1.51k, libspatialindex v1.8.5, libspatialite v4.3.0a, M4 v1.4.18, - Mono v4.8.0.495, MyMediaLite v3.12, PGI v17.1, PROJ v4.9.3, PyQt v4.12, QCA v2.1.3, QwtPolar v1.1.1, Qwt v6.1.3, - requests v2.13.0, SIP v4.19, SPAdes v3.10.1, STAR v2.5.2b, SWASH v4.01, SWIG v3.0.11, Tensorflow v1.0.1, - ViennaRNA 2.3.4, Yasm v1.3.0 + L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307, #4332), QJson (#4305), + QScintilla (#4306, #4313), sketchmap (#4360), snaphu (#4362) +- added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4 - various enhancements, including: - fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318) - - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) - various bug fixes, including: - - fix missing PYTHONPATH in ROOT v6.08.02 easyconfig (#4239) + - correctly set $PYTHONPATH in ROOT easyconfigs (#4239, #4331) - correct libjpeg turbo references in GDAL (#4276) - - fix to be sure the HDF5 provided by easybuild is used in BLASR (#4278) - - miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... (#4291) - - fix shebang in miRDeep2 Perl scripts (#4301) - - also check with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) - - also copy Rfam_for_miRDeep.fa to mirDeep2 directory (#4316) + - make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (#4278) + - fix issues with miRDeep2 installation (#4291, #4301, #4316) + - also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - fix PostgreSQL homepage + minor style fixes (#4318) - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) - - correctly set $PYTHONPATH in ROOT easyconfigs (#4331) - - add requests and psycopg2 as dependencies for QGIS (#4332) + - fix homepage/source_urls for ViennaRNA (#4338) + - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) + - remove include/GL/wglext.h from Mesa sanity check (#4354) v3.1.1 (March 7th 2017) ----------------------- -bugfix release +bugfix/update release - added example easyconfig files for 16 new software packages: - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246), diff --git a/setup.py b/setup.py index 0683e432c9..0512590286 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.0.dev0' +VERSION = '3.1.2' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 4b402eaee4aa4427376aa3ab0871650e6e87758e Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:24:22 +0000 Subject: [PATCH 564/818] cannot have directories with trailing dot in windows --- .../s/{S.A.G.E. => SAGE}/S.A.G.E.-6.3.eb | 4 +-- easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb | 25 +++++++++++++++++++ 2 files changed, 27 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/{S.A.G.E. => SAGE}/S.A.G.E.-6.3.eb (79%) create mode 100644 easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb diff --git a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb similarity index 79% rename from easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb index 28ef2c7ef6..52a2bd4d13 100644 --- a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb @@ -7,14 +7,14 @@ easyblock = "Tarball" name = 'S.A.G.E.' version = '6.3' -homepage = 'https://code.google.com/archive/p/opensage/' +homepage = 'http://darwin.cwru.edu/sage/' description = """ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/opensage/'] +source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb new file mode 100644 index 0000000000..7935579b22 --- /dev/null +++ b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'S.A.G.E.' +version = '6.4' + +homepage = 'http://darwin.cwru.edu/sage/' +description = """ S.A.G.E. (Statistical Analysis for Genetic +Epidemiology) is free software package containing programs for +use in the genetic analysis of family, pedigree and individual data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://darwin.cwru.edu/sage/files/'] +sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/freq", "bin/ageon", "bin/segreg"], + 'dirs': ["data_files", "documentaion"] +} + +moduleclass = 'bio' -- GitLab From 13f84a024104777d4ef6d6aa90f158b1d37a6589 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:31:51 +0000 Subject: [PATCH 565/818] rename so everything uses the non-dot names --- easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.3.eb => SAGE-6.3.eb} | 4 ++-- easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.4.eb => SAGE-6.4.eb} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.3.eb => SAGE-6.3.eb} (90%) rename easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.4.eb => SAGE-6.4.eb} (90%) diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb similarity index 90% rename from easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 52a2bd4d13..3ff2689829 100644 --- a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -4,7 +4,7 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' version = '6.3' homepage = 'http://darwin.cwru.edu/sage/' @@ -15,7 +15,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb similarity index 90% rename from easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index 7935579b22..fa85d69211 100644 --- a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -4,7 +4,7 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' version = '6.4' homepage = 'http://darwin.cwru.edu/sage/' @@ -15,7 +15,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://darwin.cwru.edu/sage/files/'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], -- GitLab From 56f97bf6c0649519fd493ee0861496d065da3209 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:43:24 +0000 Subject: [PATCH 566/818] updating with checksums --- easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb | 1 + easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 3ff2689829..603afb8db8 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['c94a0b9af656212251ce452f7b2f99ec'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index fa85d69211..f518617128 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://darwin.cwru.edu/sage/files/'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['da3b135389df1ab9a21288cb041ac0c3'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], -- GitLab From d6dc1c333d65c9336a6f0ccd622a6c05d0e0bbbe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2017 16:40:08 +0100 Subject: [PATCH 567/818] include #4368 in v3.1.2 release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1faff06d0d..a56c5c3afe 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -30,6 +30,7 @@ bugfix/update release - fix homepage/source_urls for ViennaRNA (#4338) - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) - remove include/GL/wglext.h from Mesa sanity check (#4354) + - rename S.A.G.E. to SAGE, can't have directories with trailing dot in Windows (#4368) v3.1.1 (March 7th 2017) -- GitLab From d7ce8c79da296aef4c19d2b976caa770d7552fbc Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 15:43:15 +0000 Subject: [PATCH 568/818] update with version variable --- easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 603afb8db8..3c539b01d1 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -14,7 +14,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] +source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v%(version)s'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] checksums = ['c94a0b9af656212251ce452f7b2f99ec'] -- GitLab From ecc192ceba36db967ebf16ba3ac1131f0f1c1ec4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Mar 2017 18:29:56 +0100 Subject: [PATCH 569/818] add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs --- .../easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-foss-2015a.eb | 2 +- .../l/libunwind/libunwind-1.1-foss-2016a.eb | 1 + .../l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 1 + .../l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 1 + .../l/libunwind/libunwind-1.1-intel-2016b.eb | 1 + 6 files changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 6bc89f03e7..43105b8275 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,6 +15,16 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index 15053fb3db..fe52e32d1e 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index ac65492ae4..24e009d090 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 6d87f10400..daf551f8aa 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 6e07f18865..aae5a5fed7 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index aea3c64e51..e201bb7758 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } -- GitLab From ccf4d6591d7369bbba30a1af83fa1de8219b39d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Mar 2017 18:57:45 +0100 Subject: [PATCH 570/818] add missing XZ easyconfig --- .../easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb new file mode 100644 index 0000000000..0423282a10 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +patches = ['XZ-%(version)s_compat-libs.patch'] + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', '0.19.8', '', True), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 2311bc03eae3c5cf5562baff913f2b366e778a45 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 20 Mar 2017 10:09:29 +0100 Subject: [PATCH 571/818] fix freetype dependency and moduleclass --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index d40917cf4c..e7e4443ff3 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), ('ROOT','v6.08.02','-Python-%(pyver)s'), - ('matplotlib', '1.5.1', '-Python-%(pyver)s') + ('matplotlib', '1.5.1', '-freetype-2.6.3') ] sanity_check_paths = { @@ -29,4 +29,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'bio' +moduleclass = 'data' -- GitLab From cc70804b27f7ce9391e362ed0f27237036e51aed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 20 Mar 2017 10:18:39 +0100 Subject: [PATCH 572/818] adding easyconfigs: QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb --- .../QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..703fb053f6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'QuTiP' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://qutip.org' +description = """QuTiP is open-source software for simulating the dynamics of open quantum systems.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://qutip.org/downloads/%(version)s/'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From a797616eb175ed6650e8247579bb4f1a2f0fcbef Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 12:37:28 +0100 Subject: [PATCH 573/818] Bowtie2 - With a patch to change the Makefile to use better compiler options for Intel, also based on a suggestion on the Allinea blog --- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 45 +++++++++++++++++++ .../Bowtie2-2.2.9_optimize-intel.patch | 22 +++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb new file mode 100644 index 0000000000..3817ce9c24 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp: Patch for better optimization with the +# Intel compilers, based on +# https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.9' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +patches = ['Bowtie2-%(version)s_optimize-intel.patch'] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "LICENSE", "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch new file mode 100644 index 0000000000..7c5a3cf076 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch @@ -0,0 +1,22 @@ +# Adapt Bowtie2 makefile to use compiler flags that are suited for icpc. +# Options are derived from the options that EasyBuild choses. +# In particular, the compile is no longer restricted to SSE2 but now +# uses -xHost so that AVX/AVX2 instructions will be attempted were appropriate, +# as suggested by https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance +# Author: Kurt Lust, UAntwerp. +--- bowtie2-2.2.9-orig/Makefile 2016-03-10 16:15:50.000000000 +0100 ++++ bowtie2-2.2.9/Makefile 2017-03-20 11:06:20.521070416 +0100 +@@ -165,11 +165,9 @@ + $(error bowtie2 compilation requires a 64-bit platform ) + endif + +-SSE_FLAG=-msse2 +- +-DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) ++DEBUG_FLAGS = -std=c++11 -O0 -g3 -xHost -ftz -fp-speculation=safe -fp-model source + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" +-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 ++RELEASE_FLAGS = -std=c++11 -O2 -xHost -ftz -fp-speculation=safe -fp-model source + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -- GitLab From 8a32fc2baa2a1f2e1780adbc366e0ecf34401c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 13:20:17 +0100 Subject: [PATCH 574/818] adding easyconfigs: imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb --- ...ed-learn-0.2.1-intel-2016b-Python-3.5.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..399d48b06b --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('scikit-learn', '0.18.1', versionsuffix), +] + +options = {'modulename': 'imblearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 2e7c9ddb5a373c9ffdb28645e29f2708c8380efb Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 14:02:30 +0100 Subject: [PATCH 575/818] Bowtie2 for Intel: Changed the easyconfig so that the patch from the previous commit is not needed; removed the patch. --- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 6 ++++- .../Bowtie2-2.2.9_optimize-intel.patch | 22 ------------------- 2 files changed, 5 insertions(+), 23 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 3817ce9c24..28ad38c224 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -27,7 +27,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -patches = ['Bowtie2-%(version)s_optimize-intel.patch'] +toolchainopts = {'cstd': 'c++11'} + +# Make sure that the Makefile uses options for intel rather than the ones for gcc coded +# in the Makefile by setting RELEASE_FLAGS. +buildopts = 'RELEASE_FLAGS="$CXXFLAGS"' files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch deleted file mode 100644 index 7c5a3cf076..0000000000 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch +++ /dev/null @@ -1,22 +0,0 @@ -# Adapt Bowtie2 makefile to use compiler flags that are suited for icpc. -# Options are derived from the options that EasyBuild choses. -# In particular, the compile is no longer restricted to SSE2 but now -# uses -xHost so that AVX/AVX2 instructions will be attempted were appropriate, -# as suggested by https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance -# Author: Kurt Lust, UAntwerp. ---- bowtie2-2.2.9-orig/Makefile 2016-03-10 16:15:50.000000000 +0100 -+++ bowtie2-2.2.9/Makefile 2017-03-20 11:06:20.521070416 +0100 -@@ -165,11 +165,9 @@ - $(error bowtie2 compilation requires a 64-bit platform ) - endif - --SSE_FLAG=-msse2 -- --DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) -+DEBUG_FLAGS = -std=c++11 -O0 -g3 -xHost -ftz -fp-speculation=safe -fp-model source - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" --RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 -+RELEASE_FLAGS = -std=c++11 -O2 -xHost -ftz -fp-speculation=safe -fp-model source - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" - NOASSERT_FLAGS = -DNDEBUG - FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -- GitLab From 379f4c31ce260b1cbc92362a30c6426e81c4ef14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 14:19:45 +0100 Subject: [PATCH 576/818] adding easyconfigs: SWASH-3.14-intel-2016b-mpi.eb, SWASH-3.14-intel-2017a-mpi.eb --- .../s/SWASH/SWASH-3.14-intel-2016b-mpi.eb | 31 +++++++++++++++++++ .../s/SWASH/SWASH-3.14-intel-2017a-mpi.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb new file mode 100644 index 0000000000..82347e4014 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb new file mode 100644 index 0000000000..6b97716f50 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' -- GitLab From 69933991035c5ce2ac99a843390487cd68109eca Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 14:38:47 +0100 Subject: [PATCH 577/818] Bowtie2: Modified the comments as requested in the pull request comments. --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 28ad38c224..fa3d31dfa4 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -6,9 +6,8 @@ # Ottawa Hospital Research Institute - Bioinformatics Team # Modified by: Adam Huffman # The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp: Patch for better optimization with the -# Intel compilers, based on -# https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance +# Modified by: Kurt Lust, UAntwerp: Overwrite compiler options used in the GNU-based +# Makefile with the preferred options for intel compilers. easyblock = 'MakeCp' -- GitLab From b97f2f6df4dd995e89280b15598056f4c66db77c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 15:11:03 +0100 Subject: [PATCH 578/818] adding easyconfigs: EasyBuild-3.1.2.eb --- .../e/EasyBuild/EasyBuild-3.1.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb new file mode 100644 index 0000000000..eaadea3b41 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.2' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/ef/c7/640c6d791ba452321c0d1371b6626486bb495e0645bb896d33c78a09f810', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/fa/00/6a47862b38e6d921071d305deab4c494ae2eae58556c90c95e520fea28b9/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/d6/55/9b6634b01fbc26edb9f5af39b06acbe7ec843da438ba5ac3063937934b3e', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/5a/4c/ea8faa46c7874a3d20f28e2d222a1f4a5e97a4f8052add338a785755ec89', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.25.tar.gz', + 'vsc-base-2.5.7.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 80350c7b4c07f77f07a1b646bbc4f45cec83d619 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 18:06:38 +0100 Subject: [PATCH 579/818] bump version to v3.2.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0512590286..0683e432c9 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.1.2' +VERSION = '3.2.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From bf8085add933e30949220dbef4b6caba7ab1c34c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 21 Mar 2017 15:19:13 +0800 Subject: [PATCH 580/818] adding easyconfigs: QuantumESPRESSO-6.1-intel-2017a.eb --- .../QuantumESPRESSO-6.1-intel-2017a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb new file mode 100644 index 0000000000..4a105c34ef --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb @@ -0,0 +1,59 @@ +name = 'QuantumESPRESSO' +version = '6.1' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-2.1.0.tar.gz', + 'qe-gipaw-6.1.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + # 'plumed-1.3-qe-r11758.tar.gz', + 'want-2.5.1-base.tar.gz', + 'West-2.0.1.tar.gz', + 'yambo-3.4.2.tgz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/240/1075/', # qe-6.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://www.west-code.org/downloads/', # West-2.0.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/208/932/', # yambo-3.4.2.tgz +] + +patches = [ + 'QuantumESPRESSO-5.4.0_yambo-fixes.patch', +] + +# source checksums +checksums = [ + 'db398edcad76e085f8c8a3f6ecb7aaab', # qe-6.1.tar.gz + '07a81c002b41d6d0f97857e55c57d769', # wannier90-2.1.0.tar.gz + '178055353e59eb4dd8bebe27331f2927', # qe-gipaw-6.1.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '000abe6a5dccd1e722d1767c3dcd3996', # West-2.0.1.tar.gz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz +] + +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +buildopts = 'all w90 epw gipaw want west yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From 0a20d53f1dc9beebcf2f9938f2d84c9963a997a3 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 21 Mar 2017 11:00:13 +0100 Subject: [PATCH 581/818] fix versionsuffix dependency matplotlib --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index e7e4443ff3..efecae95e8 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), ('ROOT','v6.08.02','-Python-%(pyver)s'), - ('matplotlib', '1.5.1', '-freetype-2.6.3') + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3') ] sanity_check_paths = { -- GitLab From d1b093ed3d64f2b8d2bf4a6c35a9f356da607c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 13:06:07 +0100 Subject: [PATCH 582/818] sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock --- .../b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb | 7 +++--- .../b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb | 7 +++--- .../b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 8 +------ .../b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 8 +------ .../b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 12 +--------- .../b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb | 3 +-- .../b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 22 ++----------------- 19 files changed, 26 insertions(+), 197 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb index 13ddeb08e1..f334c5a116 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb @@ -12,17 +12,18 @@ name = 'Bowtie2' version = '2.0.2' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge + +# to add scripts folder to $PATH just uncomment this line +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb index 7f8fbd5ca6..fa8a4e145b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb @@ -12,7 +12,6 @@ name = 'Bowtie2' version = '2.0.2' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool @@ -20,10 +19,12 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge + +# to add scripts folder to $PATH just uncomment this line +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 9469af37f5..a81247d559 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.0.5' @@ -16,6 +14,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] @@ -24,11 +23,6 @@ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), "doc", "example", "scripts"] -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 264b5296c0..00cfc5cb06 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.0.6' @@ -16,6 +14,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] @@ -24,11 +23,6 @@ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), "doc", "example", "scripts"] -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index f3e4ae2e16..8f006d9054 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.1.0' @@ -16,19 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), - "doc", "example", "scripts"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb index 975220fa34..de611ce79f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb @@ -12,14 +12,13 @@ name = 'Bowtie2' version = '2.1.0' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2', '2.1.0'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} # note: SOURCEFORGE_SOURCE constant doesn't work here because of bowtie-bio used in URL source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 3ccec7b3ec..9dc4955f2b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.0' @@ -16,20 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index 37790b2b2b..535fcdd94e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.2' @@ -16,20 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index 48fab89b05..8e2370c316 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.4' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index 3f2240e2f4..b011315af8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.5' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index 0bb8d3c531..4dca70247f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.5' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index ab7844bff7..6cd8cef8b8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.6' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 9167bcb56a..5c6e44e1e9 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.6' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index 063d865aaf..7cd080fdb1 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.7' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb index 7309705748..e6c1bebf90 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.8' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb index 4a280ff234..4982ab4d19 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.8' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb index 7f469a05ee..cf2e82b71c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.9' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb index c03250720b..637e625710 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = "2.2.9" @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index fa3d31dfa4..826bc88a15 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -6,10 +6,7 @@ # Ottawa Hospital Research Institute - Bioinformatics Team # Modified by: Adam Huffman # The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp: Overwrite compiler options used in the GNU-based -# Makefile with the preferred options for intel compilers. - -easyblock = 'MakeCp' +# Modified by: Kurt Lust, UAntwerp name = 'Bowtie2' version = '2.2.9' @@ -22,26 +19,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -toolchainopts = {'cstd': 'c++11'} - -# Make sure that the Makefile uses options for intel rather than the ones for gcc coded -# in the Makefile by setting RELEASE_FLAGS. -buildopts = 'RELEASE_FLAGS="$CXXFLAGS"' - -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "LICENSE", "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line #modextrapaths = {'PATH': 'scripts'} -- GitLab From e5d137194f7e4d46ed8578d0a0a25f4c2c4be089 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:25:53 +0100 Subject: [PATCH 583/818] adding easyconfigs: JasPer-2.0.12-intel-2017a.eb --- .../j/JasPer/JasPer-2.0.12-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb new file mode 100644 index 0000000000..668f15ccad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.12' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/jasper', 'lib64/libjasper.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'vis' -- GitLab From 721d136ab9753a345adfd377e5f391fbd0e97833 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:40:34 +0100 Subject: [PATCH 584/818] adding easyconfigs: HDF5-1.10.0-patch1-intel-2017a.eb, Szip-2.1-intel-2017a.eb --- .../h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb | 22 ++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2017a.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb new file mode 100644 index 0000000000..bc132a2144 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb new file mode 100644 index 0000000000..7a02acddee --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From b5f873be346781802822e6f839239e35ebb22dff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:49:54 +0100 Subject: [PATCH 585/818] adding easyconfigs: netCDF-4.4.1.1-intel-2017a.eb, netCDF-Fortran-4.4.4-intel-2017a.eb, cURL-7.53.1-GCCcore-6.3.0.eb, Doxygen-1.8.13-GCCcore-6.3.0.eb --- .../c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb | 34 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb | 23 +++++++++++++ .../netCDF-Fortran-4.4.4-intel-2017a.eb | 17 ++++++++++ .../n/netCDF/netCDF-4.4.1.1-intel-2017a.eb | 34 +++++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..09811fccde --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.53.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..00e9535d4b --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +name = 'Doxygen' +version = '1.8.13' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb new file mode 100644 index 0000000000..fa3d6fe963 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb new file mode 100644 index 0000000000..d30a65ec63 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.10.0-patch1'), + ('cURL', '7.53.1'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 5762444b72a33f59fe9ba453c4d5eca6ffb80f25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 16:31:10 +0100 Subject: [PATCH 586/818] collapse checksums to a single line to make @wpoely86 happy --- easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 4 +--- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb | 4 +--- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb | 4 +--- 6 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 43105b8275..396cb5364f 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index fe52e32d1e..19a10c8362 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,9 +15,7 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 24e009d090..9cbc7f2bbf 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index daf551f8aa..97bdf43906 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,9 +15,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index aae5a5fed7..5b2faed557 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index e201bb7758..ba5d709769 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), -- GitLab From 1e610f306de5153e933712cb219a377d1dfe9947 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 19:49:40 +0100 Subject: [PATCH 587/818] use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb index aba6939866..f931b781ea 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb @@ -15,8 +15,8 @@ source_urls = [homepage] # see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False -# compilation fails when configuring with --enable-avx-128-fma -use_fma = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False runtest = 'check' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb index 07c5fa9224..da857e5ca5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -21,8 +21,8 @@ patches = [ # http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False -# compilation fails when configuring with --enable-avx-128-fma -use_fma = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False runtest = 'check' -- GitLab From baae366171417e854889d108e8f266afeaec8e98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 22:26:58 +0100 Subject: [PATCH 588/818] adding easyconfigs: WRF-3.8.0-intel-2016b-dmpar.eb, tcsh-6.20.00-GCCcore-5.4.0.eb --- .../t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 41 +++++++++++++++++++ .../w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..1413bb1d34 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.20.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb new file mode 100644 index 0000000000..9f07b0effa --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '3.8.0' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.10'), + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF_tests_limit-runtimes.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRF-%(version)s_known_problems.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' -- GitLab From b8c0b56d34346a63dbd7933630ad5ef2e8e68299 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 22:39:04 +0100 Subject: [PATCH 589/818] fix netCDF version in dependencies --- easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb index 9f07b0effa..09959e26a3 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb @@ -22,7 +22,7 @@ builddependencies = [('tcsh', '6.20.00')] dependencies = [ ('JasPer', '2.0.10'), - ('netCDF', '4.4.1.1'), + ('netCDF', '4.4.1'), ('netCDF-Fortran', '4.4.4'), ] -- GitLab From 800c673582b5a3203d6a073f4a2800e82199ee9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Mar 2017 20:04:21 +0100 Subject: [PATCH 590/818] adding easyconfigs: ACTC-1.1-intel-2016b.eb --- .../a/ACTC/ACTC-1.1-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb new file mode 100644 index 0000000000..88e0e00942 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +installopts = "INCDEST=%(installdir)s/include/ac/ LIBDEST=%(installdir)s/lib && " +installopts += "mv %(installdir)s/lib/tc.h %(installdir)s/include/ac/ && " +installopts += "mkdir %(installdir)s/bin && cp -a {tcsample,tctest,tctest2} %(installdir)s/bin && " +installopts += "cp -a {COPYRIGHT,manual.html,prims.gif,README} %(installdir)s/" + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 933287b2503f1828df80efc7277958dcf53f559f Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Mar 2017 19:21:18 +0000 Subject: [PATCH 591/818] renamed recipe to match convention --- ...2016a-download.eb => PETSc-3.7.5-intel-2016a-download_deps.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-download.eb => PETSc-3.7.5-intel-2016a-download_deps.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb -- GitLab From cb193298f3defbc6c268e7e7f2aa6f1f42156fdf Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Mar 2017 19:21:59 +0000 Subject: [PATCH 592/818] renamed recipe to match convention --- ...ownload_deps.eb => PETSc-3.7.5-intel-2016a-downloaded_deps.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-download_deps.eb => PETSc-3.7.5-intel-2016a-downloaded_deps.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb -- GitLab From d78a9a2c5fb56e58eb9c44aa60ad3365b503b0d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 10:26:12 +0100 Subject: [PATCH 593/818] adding easyconfigs: OpenMPI-2.1.0-GCC-6.3.0-2.28.eb, hwloc-1.11.6-GCC-6.3.0-2.28.eb, GCC-6.3.0-2.28.eb --- easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb | 25 ++++++++++++++ .../h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb | 23 +++++++++++++ .../o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb | 34 +++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..bac0785b8c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.3.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..93ceada29d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.6' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..f0864ac518 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.1.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['c058052b53d209c7521079e3d2da613b'] + +dependencies = [('hwloc', '1.11.6')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' -- GitLab From 3f38e052bc47c21c631e125a8bf556792bce9e0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 11:26:13 +0100 Subject: [PATCH 594/818] correctly update $CPATH in ACTC easyconfig --- easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb index 88e0e00942..c94517dc29 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = {'CPATH': 'include/ac'} + moduleclass = 'lib' -- GitLab From 5d143002ba0dde7c4e197453c88c488e9c431ea8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 11:49:15 +0100 Subject: [PATCH 595/818] adding easyconfigs: HISAT2-2.0.5-intel-2017a.eb, NGS-1.3.0-intel-2017a.eb, ncbi-vdb-2.8.2-intel-2017a.eb, file-5.30-intel-2017a.eb --- .../f/file/file-5.30-intel-2017a.eb | 25 ++++++++++++ .../h/HISAT2/HISAT2-2.0.5-intel-2017a.eb | 36 ++++++++++++++++++ .../n/NGS/NGS-1.3.0-intel-2017a.eb | 35 +++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb | 38 +++++++++++++++++++ 4 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb new file mode 100644 index 0000000000..cab481c6f4 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.30' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb new file mode 100644 index 0000000000..a0d6f2ef27 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.5' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +patches = ['HISAT2-%(version)s_intel-fixes.patch'] + +checksums = ['b6d867e1f8463012d1de3d1472573906'] + +dependencies = [ + ('NGS', '1.3.0'), + ('ncbi-vdb', '2.8.2'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb new file mode 100644 index 0000000000..8d0219a742 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.3.0' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_121', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb new file mode 100644 index 0000000000..5bfe59a4db --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.8.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.30'), # provides libmagic + ('HDF5', '1.10.0-patch1'), + ('NGS', '1.3.0'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 399938d27b6370d98c81312cd0c3699e76360be8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:20:18 +0100 Subject: [PATCH 596/818] add missing patch file for HISAT2 --- .../h/HISAT2/HISAT2-2.0.5_intel-fixes.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch new file mode 100644 index 0000000000..571fc956b3 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch @@ -0,0 +1,15 @@ +fix Intel compiler error due to wrong cast to void*, should be int* +author: Kenneth Hoste (HPC-UGent) +--- hisat2-2.0.5/processor_support.h.orig 2017-03-23 11:39:02.647104669 +0100 ++++ hisat2-2.0.5/processor_support.h 2017-03-23 11:39:23.727376802 +0100 +@@ -44,8 +44,8 @@ + + try { + #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) +- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception +- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX ++ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception ++ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else -- GitLab From 0caaed423383193b70eb9765c15c4d55ba479f66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:21:08 +0100 Subject: [PATCH 597/818] {bio}[intel/2017a] SAMtools 1.4 --- .../s/SAMtools/SAMtools-1.4-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb new file mode 100644 index 0000000000..86a737bc61 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), +] + +moduleclass = 'bio' -- GitLab From f9903bade05e9e83af1538b4ebe64a3916fc55cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:21:29 +0100 Subject: [PATCH 598/818] also patch XZ 5.2.3 to include symbols required by rpm command --- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 0e517cfb0f..735c3cbe5b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-5.2.2_compat-libs.patch'] + builddependencies = [ ('gettext', '0.19.8.1', '', True), # use same binutils version that was used when building GCCcore toolchain -- GitLab From 732a70a17a353521a2a9128c5acb8d766c06417c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 13:43:23 +0100 Subject: [PATCH 599/818] use MakeCp for ACTC --- .../easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb index c94517dc29..47b6a5d46f 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'ACTC' version = '1.1' @@ -11,14 +11,14 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -skipsteps = ['configure'] - buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' -installopts = "INCDEST=%(installdir)s/include/ac/ LIBDEST=%(installdir)s/lib && " -installopts += "mv %(installdir)s/lib/tc.h %(installdir)s/include/ac/ && " -installopts += "mkdir %(installdir)s/bin && cp -a {tcsample,tctest,tctest2} %(installdir)s/bin && " -installopts += "cp -a {COPYRIGHT,manual.html,prims.gif,README} %(installdir)s/" +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] sanity_check_paths = { 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', -- GitLab From 27497f51ac83dddbba0c8be081f7d94ebe9a26d1 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 23 Mar 2017 13:07:11 +0000 Subject: [PATCH 600/818] changed toolchain so that HDF5 1.8.18 is found by the bot --- ...oaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded_deps.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-downloaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded_deps.eb} (96%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb similarity index 96% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb index 111a8d2edd..f864b6e767 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb @@ -6,7 +6,7 @@ homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] -- GitLab From cd45943e036bb52b2bab419b4d529947949eb272 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 14:30:07 +0100 Subject: [PATCH 601/818] {vis}[intel/2016b] VMD 1.9.3 --- .../v/VMD/VMD-1.9.3-intel-2016b.eb | 34 +++++ .../v/VMD/VMD-1.9.3_configure.patch | 116 ++++++++++++++++++ 2 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb new file mode 100644 index 0000000000..2a5279436b --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +name = 'VMD' +version = '1.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain= {'name': 'intel' , 'version': '2016b'} + +# downloading requires registration +sources = [('%(namelower)s-%(version)s.src.tar.gz', "tar xfv %s")] + +patches = [ + 'VMD-%(version)s_configure.patch', +] + +dependencies = [ + ('Tcl', '8.6.5'), + ('Tk', '8.6.5'), + ('FLTK', '1.3.3'), + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), + ('netCDF', '4.4.1.1'), + ('FFmpeg', '3.1.3'), + ('ImageMagick', '7.0.3-1'), + ('ACTC', '1.1'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch new file mode 100644 index 0000000000..23f1311b5b --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch @@ -0,0 +1,116 @@ +fix hardcoded stuff in VMD configure script +authors: Stephane Thiell (Stanford University), Kenneth Hoste (HPC-UGent) +--- vmd-1.9.3/configure.orig 2016-12-01 08:11:33.000000000 +0100 ++++ vmd-1.9.3/configure 2017-03-23 13:36:41.501910996 +0100 +@@ -466,7 +476,7 @@ + + $arch_cc = "cc"; + $arch_ccpp = "CC"; +-$arch_nvcc = "/usr/local/cuda-8.0/bin/nvcc"; ++$arch_nvcc = "nvcc"; + $arch_nvccflags = "--ptxas-options=-v " . + "-gencode arch=compute_30,code=compute_30 " . + "-gencode arch=compute_30,code=sm_35 " . +@@ -581,17 +591,17 @@ + # location of Mesa library and include files; basically does the same + # as OpenGL. This is based on the default instructions from the Mesa + # README; the include files should by default be in /usr/local/include/GL. +-$mesa_dir = "$vmd_library_dir/Mesa"; ++$mesa_dir = $ENV{'EBROOTMESA'}; + $mesa_include = "-I$mesa_dir/include"; + $mesa_library = "-L$mesa_dir/lib_$config_arch"; + #$mesa_libs = "-lMesaGL -lMesaGLU"; +-$mesa_libs = "-lMesaGL"; ++$mesa_libs = "-lGL -lGLU"; + $mesa_defines = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL"; + @mesa_cc = (); + @mesa_cu = (); +-@mesa_ccpp = @opengl_ccpp; +-@mesa_h = @opengl_h; +-@mesa_extra = @opengl_extra; ++@mesa_ccpp = (); ++@mesa_h = (); ++@mesa_extra = (); + + + # +@@ -666,10 +676,10 @@ + + ################ FLTK GUI + $fltk_defines = "-DVMDGUI -DVMDFLTK"; +-$fltk_dir = "$vmd_library_dir/fltk"; ++$fltk_dir = $ENV{'EBROOTFLTK'}; + $fltk_include = "-I$fltk_dir/include"; + $fltk_library = "-L$fltk_dir/$config_arch"; +-$fltk_libs = "-lfltk -lX11"; ++$fltk_libs = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama"; + #@fltk_cc = ('forms_ui.c'); + @fltk_cu = (); + @fltk_ccpp = ( 'ColorFltkMenu.C', +@@ -729,8 +739,8 @@ + if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } + $tcl_library = "-L$stock_tcl_library_dir"; + if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } +-$tcl_libs = "-ltcl8.5"; +-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } ++$tcl_libs = "-ltcl8.6"; ++if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; } + + @tcl_cc = (); + @tcl_cu = (); +@@ -922,7 +932,7 @@ + # This option enables the use of CUDA GPU acceleration functions. + ####################### + $cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA"; +-$cuda_dir = "/usr/local/cuda-8.0"; ++$cuda_dir = "$CUDA_HOME"; + $cuda_include = ""; + $cuda_library = ""; + $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static"; +@@ -1042,7 +1052,7 @@ + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.6.3-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.8.0-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.9.0-linux64"; +-$liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-4.0.1-linux64"; ++$liboptix_dir = "$ENV{'EBROOTOPTIX'}"; + # NCSA Blue Waters + # $liboptix_dir = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.6.3-linux64"; + # $liboptix_dir = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.8.0-linux64"; +@@ -1310,8 +1320,8 @@ + ####################### + $actc_defines = "-DVMDACTC"; + $actc_dir = "$vmd_library_dir/actc"; +-$actc_include = "-I$actc_dir/include"; +-$actc_library = "-L$actc_dir/lib_$config_arch"; ++$actc_include = "-I$actc_dir"; ++$actc_library = "-L$actc_dir"; + $actc_libs = "-lactc"; + @actc_cc = (); + @actc_cu = (); +@@ -1388,7 +1398,7 @@ + $python_defines = "-DVMDPYTHON"; + $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir"; + $python_library = "-L$stock_python_library_dir"; +-$python_libs = "-lpython2.5 -lpthread"; ++$python_libs = "-lpython2.7 -lpthread"; + @python_h = ('PythonTextInterp.h', + 'VMDTkinterMenu.h', + 'py_commands.h', +@@ -2173,7 +2183,7 @@ + + if ($config_static) { + $arch_lopts = "-static"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } else { + $arch_lopts = ""; + # -rpath causes problems for people running Chromium.. +@@ -2303,7 +2313,7 @@ + # they likely serve no useful purpose going forward. + if (!$config_opengl_dispatch) { + $opengl_dep_libs = "-L/usr/X11R6/lib64 -lGL -lX11"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } + + # this is to make tcl happy -- GitLab From 84b686e27ad0f9e554a6cf078d652a77c11913b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 17:03:48 +0100 Subject: [PATCH 602/818] style fixes in PETSc easyconfig that downloads deps --- ...ETSc-3.7.5-intel-2016b-downloaded-deps.eb} | 31 ++++++------------- 1 file changed, 9 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016b-downloaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded-deps.eb} (68%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb similarity index 68% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb index f864b6e767..87e4b65750 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb @@ -1,6 +1,6 @@ name = 'PETSc' version = '3.7.5' -versionsuffix = '-downloaded_deps' +versionsuffix = '-downloaded-deps' homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -12,32 +12,19 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] +# (build) dependencies provided through EasyBuild builddependencies = [('CMake', '3.5.2')] -shared_libs = 1 -pic = 1 - -downloadinstall = True - -# For these dependencies, we do not download them dependencies = [('HDF5','1.8.18')] -configopts = "" -configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " -configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" # external packages that are downloaded with --download-=1 and --download--static=1 -download_deps_static = [ - 'hypre', - 'metis', - 'ml', - 'mumps', - 'parmetis', - 'prometheus', - 'ptscotch', - 'suitesparse', - 'superlu', - 'superlu_dist' -] +download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', + 'superlu', 'superlu_dist'] # triangle cannot be downloaded with --download-triangle-static because it fails download_deps = ['triangle'] +configopts = "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +shared_libs = True + moduleclass = 'numlib' -- GitLab From bca436c37aa54ec9ae171066f4d480a701f664f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 17:41:36 +0100 Subject: [PATCH 603/818] add checksum for VMD 1.9.3 sources --- easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb index 2a5279436b..3e3df4bec4 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb @@ -13,11 +13,11 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain= {'name': 'intel' , 'version': '2016b'} # downloading requires registration -sources = [('%(namelower)s-%(version)s.src.tar.gz', "tar xfv %s")] +sources = ['vmd-%(version)s.src.tar.gz'] -patches = [ - 'VMD-%(version)s_configure.patch', -] +patches = ['VMD-%(version)s_configure.patch'] + +checksums = ['5706f88b9b77cc5fafda6fef3a82d6fa'] dependencies = [ ('Tcl', '8.6.5'), -- GitLab From 3d41143457e45e0b7c720954adf981364f9ab72a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 18:44:18 +0100 Subject: [PATCH 604/818] fix easyconfig filename for VMD --- ....9.3-intel-2016b.eb => VMD-1.9.3-intel-2016b-Python-2.7.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/VMD/{VMD-1.9.3-intel-2016b.eb => VMD-1.9.3-intel-2016b-Python-2.7.12.eb} (100%) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb rename to easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb -- GitLab From 3e03d88c9300b4a346ca39a28fbbad235b9e75f7 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 24 Mar 2017 12:33:43 -0400 Subject: [PATCH 605/818] Added SAMtools-1.4-goolf-1.4.10.eb and ncurses-6.0-goolf-1.4.10.eb, the second one is a dependece of the first. By Daniel Navarro-Gomez, MEEI Bioinformatics Center new file: easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb new file: easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb --- .../n/ncurses/ncurses-6.0-goolf-1.4.10.eb | 38 ++++++++++++++++++ .../s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb | 40 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..6b10da13e5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +# Modified for goolf-1.4.10 by: Daniel Navarro-Gomez, MEEI Bioinformatics Center (MBC) + +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..f620000661 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +# Modified for goolf-1.4.10 by: Daniel Navarro-Gomez, MEEI Bioinformatics Center (MBC) +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +# +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.7'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 8f63e326929541c6c9f8911357c81019aea0bde8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Fri, 24 Mar 2017 19:27:45 +0000 Subject: [PATCH 606/818] added recipe for repasthpc --- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..d01d3cb5a2 --- /dev/null +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'RepastHPC' +version = '2.2.0' + +homepage = 'https://repast.github.io/' +description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: +Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ["repast_hpc-%s.tgz" % version] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version] + +dependencies = [ + ('netCDF-C++','4.2'), + ('Boost', '1.60.0'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' + +sanity_check_paths = { + 'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version], + 'dirs': ['include','lib','bin/zombie', 'bin/rumor'], +} + +moduleclass = 'bio' -- GitLab From 933e11553203ffe64b2c29128734b3631ce6fe77 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 12:00:12 +0800 Subject: [PATCH 607/818] adding easyconfigs: Wannier90-2.1.0-intel-2017a.eb --- .../Wannier90/Wannier90-2.1.0-intel-2017a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb new file mode 100644 index 0000000000..4945212393 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] +checksums = ['07a81c002b41d6d0f97857e55c57d769'] + +prebuildopts = 'cp ./config/make.inc.ifort ./make.inc && ' + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 33de8679402f5de09a5ce0d7bcdb5bbddd34f302 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 18:03:08 +0800 Subject: [PATCH 608/818] adding easyconfigs: DFTB+-1.3.1-intel-2017a.eb --- .../d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb new file mode 100644 index 0000000000..35d80f5918 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'DFTB+' +version = '1.3.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the + Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been + developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with + ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of + magnitude in speed.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://www.dftb-plus.info/download/dftb-13'] # requires registration +sources = [ + 'dftbplus-%(version)s-src.tar.xz', + 'dftbplus-%(version)s-extlib.tar.xz', + 'dftbplus-%(version)s-autotest.tar.xz', +] + +checksums = [ + 'b821ed7406a2a4b35c0a48974e18667f', # dftbplus-1.3.1-src.tar.xz + '2333f1ff826a3c4776e1e77a28f17004', # dftbplus-1.3.1-extlib.tar.xz + 'abaf8a2f94c74a13a0d8d19e9b022e40', # dftbplus-1.3.1-autotest.tar.xz +] + +dependencies = [ + ('arpack-ng', '3.4.0'), +] + +subdir = '%dftbplus-%(version)s' + +prebuildopts = "sed 's/ARCH = x86_64-linux-intel/ARCH = user/' Makefile.user.template > Makefile.user && " +prebuildopts += "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " +prebuildopts += "sed -i 's|LNOPT = -static|#LNOPT = -static|' sysmakes/make.user && " +prebuildopts += "sed -i 's|/opt/intel/mkl/10.2.6.038/lib/em64t|$(MKLROOT)|' sysmakes/make.user && " +prebuildopts += "cd prg_dftb && " + +files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dftb+'], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From f9818b855274e1615306b3fde48bcbdbc3b27865 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 23:45:22 +0800 Subject: [PATCH 609/818] simplify prebuildopts --- easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb index 35d80f5918..15d96ddf6e 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -31,12 +31,11 @@ dependencies = [ subdir = '%dftbplus-%(version)s' -prebuildopts = "sed 's/ARCH = x86_64-linux-intel/ARCH = user/' Makefile.user.template > Makefile.user && " -prebuildopts += "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " -prebuildopts += "sed -i 's|LNOPT = -static|#LNOPT = -static|' sysmakes/make.user && " -prebuildopts += "sed -i 's|/opt/intel/mkl/10.2.6.038/lib/em64t|$(MKLROOT)|' sysmakes/make.user && " +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " prebuildopts += "cd prg_dftb && " +buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " + files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] sanity_check_paths = { -- GitLab From 92fd0795325dd52804826307a09bcc0fcd9cf979 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Mar 2017 17:54:49 +0200 Subject: [PATCH 610/818] adding easyconfigs: ED2-20170201-intel-2017a.eb --- .../e/ED2/ED2-20170201-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb new file mode 100644 index 0000000000..e02aad07d9 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['ED2.patch'] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "sed -i 's/^make OPT/#make OPT/g' install.sh && ./install.sh --kind E --platform intel --gitoff && " +prebuildopts += "cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' " +buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' + +files_to_copy = [(['ED/build/ed_2.1-opt'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ed_2.1-opt'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From 5ec6dcd34db0e99be4c4ba8a7cae4a12b533d4c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Mar 2017 18:18:56 +0200 Subject: [PATCH 611/818] add patches for ED2 --- .../e/ED2/ED2-20170201-intel-2017a.eb | 8 ++++--- .../easyconfigs/e/ED2/ED2_fix-type.patch | 13 ++++++++++ .../e/ED2/ED2_install-without-make.patch | 24 +++++++++++++++++++ 3 files changed, 42 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/e/ED2/ED2_fix-type.patch create mode 100644 easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb index e02aad07d9..eed367500a 100644 --- a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -14,15 +14,17 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/EDmodel/ED2/archive/'] sources = ['%s.tar.gz' % commit] -patches = ['ED2.patch'] +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] dependencies = [('HDF5', '1.10.0-patch1')] start_dir = 'ED/build' # rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options -prebuildopts = "sed -i 's/^make OPT/#make OPT/g' install.sh && ./install.sh --kind E --platform intel --gitoff && " -prebuildopts += "cd bin-opt-E && " +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' " buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' diff --git a/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch b/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch new file mode 100644 index 0000000000..4f73ca3487 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch @@ -0,0 +1,13 @@ +fix type for argument to h5dget_type_f call +see https://github.com/EDmodel/ED2/issues/153 and https://github.com/crollinson/ED2/commit/48b9e8132b992460aa8afeca222fd4c12f01cfe4 +--- ED/src/utils/hdf5_utils.F90.orig 2017-02-01 22:00:01.000000000 +0100 ++++ ED/src/utils/hdf5_utils.F90 2017-03-27 11:56:38.579744327 +0200 +@@ -432,7 +432,7 @@ + character(len=2) :: ctype + + logical :: convert = .false. +- integer :: type_id ++ integer(HID_T) :: type_id + real(kind=8), allocatable, dimension(:) :: dvaraTEMP + + ! Find which data type will be read diff --git a/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch b/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch new file mode 100644 index 0000000000..601e93e788 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch @@ -0,0 +1,24 @@ +avoid install.sh calling 'make' (and hard set GIT_EXIST) +author: Kenneth Hoste (HPC-UGent) +--- ED/build/install.sh.orig 2017-03-27 12:00:10.321077952 +0200 ++++ ED/build/install.sh 2017-03-27 11:59:40.200888391 +0200 +@@ -94,8 +94,8 @@ + esac + + # Tag executables with a git version and branch name if possible. +-GIT_EXIST=`git rev-parse --is-inside-work-tree` +-if [ ${GIT_EXIST} == "true" -a ${USE_GIT} ] ++GIT_EXIST="" ++if [ "${GIT_EXIST}" == "true" -a ${USE_GIT} ] + then + GIT_TAG=`git branch -v | awk '/\*/ {print "-" $2 "-" $3}'` + GIT_TAG=`echo ${GIT_TAG} | tr -d '()/[]'` +@@ -122,7 +122,7 @@ + touch dependency.mk + + #----- Launch the compiler. ---------------------------------------------------------------# +-make OPT=${OPT} KIND_COMP=${KIND} ${CLEAN} GIT_TAG=${GIT_TAG} ++#make OPT=${OPT} KIND_COMP=${KIND} ${CLEAN} GIT_TAG=${GIT_TAG} + make_exit_code=$? + #------------------------------------------------------------------------------------------# + -- GitLab From 1af6f173acf17c4edddfd3ce10b770e71ddb0346 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Mon, 27 Mar 2017 19:22:16 +0000 Subject: [PATCH 612/818] cosmetic changes --- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index d01d3cb5a2..d533ab1e52 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -4,25 +4,27 @@ name = 'RepastHPC' version = '2.2.0' homepage = 'https://repast.github.io/' -description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: -Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.""" +description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation +platforms that have collectively been under continuous development for over 15 years: +Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based +modeling system that is designed for use on large computing clusters and supercomputers.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -sources = ["repast_hpc-%s.tgz" % version] -source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version] +sources = ["repast_hpc-%(version)s.tgz"] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%(version)s'] dependencies = [ - ('netCDF-C++','4.2'), + ('netCDF-C++', '4.2'), ('Boost', '1.60.0'), ] configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version], - 'dirs': ['include','lib','bin/zombie', 'bin/rumor'], + 'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ], + 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } moduleclass = 'bio' -- GitLab From e64ee749935ed6de93fde54097f4bcc9caeca1b9 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 28 Mar 2017 15:29:46 +0800 Subject: [PATCH 613/818] cleanup --- easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb index 15d96ddf6e..7f8e07f325 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -29,10 +29,7 @@ dependencies = [ ('arpack-ng', '3.4.0'), ] -subdir = '%dftbplus-%(version)s' - -prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " -prebuildopts += "cd prg_dftb && " +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && cd prg_dftb && " buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " -- GitLab From a629ee133ac546cb1145364ab4dcafd4405b08f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 11:20:23 +0200 Subject: [PATCH 614/818] adding easyconfigs: WRF-Fire-20170221-intel-2016b-dmpar.eb --- .../WRF-Fire-20170221-intel-2016b-dmpar.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb new file mode 100644 index 0000000000..eeb28fe474 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -0,0 +1,23 @@ +name = 'WRF-Fire' +version = '20170221' +commit = 'f2db7a0' +buildtype = 'dmpar' +versionsuffix = '-' + buildtype + +homepage = 'http://www.openwfm.org/wiki/WRF-SFIRE' +description = """WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a + surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire + line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and + terrain slope. The fire spread is implemented by the level set method.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/openwfm/wrf-fire/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('netCDF-Fortran', '4.4.4'), +] + + +moduleclass = 'geo' -- GitLab From af3b49f341a5e52e48df92f6cfe65a3cf316c78f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 11:49:11 +0200 Subject: [PATCH 615/818] add maxparallel = 10 --- .../w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb index eeb28fe474..55b59e1608 100644 --- a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -19,5 +19,7 @@ dependencies = [ ('netCDF-Fortran', '4.4.4'), ] +# limit max. parallelism for build (WRF-Fire will cap to 2 if > 20) +maxparallel = 10 moduleclass = 'geo' -- GitLab From e9b358bfb426d73b3a04eae8b2a57dfb47e8ede6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 12:41:24 +0200 Subject: [PATCH 616/818] adding easyconfigs: Doris-4.02-intel-2017a.eb --- .../d/Doris/Doris-4.02-intel-2017a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb new file mode 100644 index 0000000000..37cf20fd5b --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.02' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' -- GitLab From b3fc425e503d838764466ab63d3321642070e1c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:31:38 +0200 Subject: [PATCH 617/818] adding easyconfigs: h5py-2.7.0-intel-2016b-Python-2.7.12.eb --- .../h5py-2.7.0-intel-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..adc15ffb81 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', '1.10.0-patch1'), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From ad6485b3fbe49817a1543a16dbb87ad2b171c876 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:32:03 +0200 Subject: [PATCH 618/818] adding easyconfigs: SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb --- ...piceyPy-1.1.0-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9ffb950100 --- /dev/null +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SpiceyPy' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AndrewAnnex/SpiceyPy' +description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' -- GitLab From 6f50fca325bea7be094393d39e28bdc2c94b19ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:32:29 +0200 Subject: [PATCH 619/818] adding easyconfigs: FFTW-3.3.6-intel-2016b.eb --- .../f/FFTW/FFTW-3.3.6-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb new file mode 100644 index 0000000000..14ebd120a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -0,0 +1,29 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' -- GitLab From 4757aa658eebdd42897f500ee38fbea0e652d2c4 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Mar 2017 12:52:24 +0000 Subject: [PATCH 620/818] escaped % --- easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index d533ab1e52..fc07069bff 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ], + 'files': ['lib/librelogo-%%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%%(version)s.%s' % SHLIB_EXT ], 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } -- GitLab From 1fd96d8483783fe062547963cb0baee7a49ed8db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 18:32:53 +0200 Subject: [PATCH 621/818] adding easyconfigs: ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb --- .../ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..367e778dfc --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ROI_PAC' +version = '3.0.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://roipac.org/' +description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data + to produce differential interferograms""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# download requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC +sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] + +# FIXME: http://roipac.org/cgi-bin/moin.cgi/Patches + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('FFTW', '3.3.6'), + ('GETORB', '2.3.2'), + ('Perl', '5.24.0'), +] + +start_dir = 'ROI_PAC' + +postinstallcmds = [ + # symlink to getorb requires in /bin subdirectory + "cd %(installdir)s/bin && ln -s $(which getorb)", + # also copy scripts and make sure they're excutable + "cp -a INT_SCR/* %(installdir)s/bin", + # fix shebang in Perl scripts + "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//bin/*.pl", +] + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/make_raw.pl', 'bin/roi'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'bin'} +modextravars = { + 'INT_BIN': '%(installdir)s/bin', + 'INT_SCR': '%(installdir)s/bin', +} + +moduleclass = 'geo' -- GitLab From fc0f4ff96ff2a60bbb800af32366c28229941270 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 18:34:36 +0200 Subject: [PATCH 622/818] adding easyconfigs: jemalloc-4.5.0-intel-2017a.eb --- .../j/jemalloc/jemalloc-4.5.0-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb new file mode 100644 index 0000000000..45f685672f --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.5.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' -- GitLab From 16bdb31b1f2f30a4a25c0a601176e39348a2a341 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 20:04:44 +0200 Subject: [PATCH 623/818] add easyconfig for GETORB dependency for ROI_PAC --- .../g/GETORB/GETORB-2.3.2-intel-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb new file mode 100644 index 0000000000..61b3b12249 --- /dev/null +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GETORB' +version = '2.3.2' + +homepage = 'http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml' +description = "GETORB software package contains programs to handle the orbital data records (ODRs)" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] +sources = ['getorb_%(version)s.tar.gz'] + +skipsteps = ['configure'] + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/lodr', 'bin/mdate'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 5ae48b9b752d2c302000a1a64f9ed58c9da4f585 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 10:31:21 +0200 Subject: [PATCH 624/818] disable parallel building for GETORB, tends to break --- easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb index 61b3b12249..2e648643f9 100644 --- a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb @@ -13,6 +13,8 @@ sources = ['getorb_%(version)s.tar.gz'] skipsteps = ['configure'] +parallel = 1 + preinstallopts = "mkdir %(installdir)s/bin && " installopts = 'BIN_DIR=%(installdir)s/bin' -- GitLab From 07b52f5f937b0962931ac68e1ff50ef6567a3ddb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 10:57:46 +0200 Subject: [PATCH 625/818] apply fixes for ROI_PAC described at http://roipac.org/cgi-bin/moin.cgi/Patches --- .../ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb index 367e778dfc..30adf12039 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -10,10 +10,14 @@ description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for pro toolchain = {'name': 'intel', 'version': '2016b'} -# download requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC +# download of ROI_PAC tarball requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] -# FIXME: http://roipac.org/cgi-bin/moin.cgi/Patches +# make_raw_alos.pl via http://roipac.org/cgi-bin/moin.cgi/ALOS_PALSAR?action=AttachFile&do=get&target=make_raw_alos.pl +patches = [ + 'ROI_PAC-%(version)s_fix-IntSim.patch', + ('make_raw_alos.pl', 'ROI_PAC/INT_SCR'), +] builddependencies = [('Autotools', '20150215')] dependencies = [ @@ -24,6 +28,8 @@ dependencies = [ start_dir = 'ROI_PAC' +installopts = "&& cd fip && $CC $CFLAGS -o add_rmgAmpPhs add_rmgAmpPhs.c && cp -a add_rmgAmpPhs %(installdir)s/bin" + postinstallcmds = [ # symlink to getorb requires in /bin subdirectory "cd %(installdir)s/bin && ln -s $(which getorb)", @@ -34,7 +40,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/getorb', 'bin/make_raw.pl', 'bin/roi'], + 'files': ['bin/add_rmgAmpPhs', 'bin/getorb', 'bin/make_raw.pl', 'bin/make_raw_alos.pl', 'bin/roi'], 'dirs': [], } -- GitLab From c1fc2295bb7312211e795a36fa9bb466465ef66d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:49:06 +0200 Subject: [PATCH 626/818] also define $MY_BIN and $ROI_PAC in ROI_PAC easyconfig --- .../r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb index 30adf12039..89a80fb749 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -48,6 +48,10 @@ modextrapaths = {'PERL5LIB': 'bin'} modextravars = { 'INT_BIN': '%(installdir)s/bin', 'INT_SCR': '%(installdir)s/bin', + 'MY_BIN': '%(installdir)s/bin', + 'ROI_PAC': '%(installdir)s', } +modloadmsg = "To define: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" + moduleclass = 'geo' -- GitLab From 58efec1edfc3367d40113a41898e9c66a597f816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:53:29 +0200 Subject: [PATCH 627/818] add easyconfig for SQLite 3.17.0 as dep for Python 2.7.13 --- .../s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..41b5a58bd2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.17.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.sqlite.org/2017/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From fb829371d5936654f861cad99145ed7ca41ab1f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:58:41 +0200 Subject: [PATCH 628/818] no need to patch libreadline 7.0 --- .../easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb index a64400af8e..66d703c987 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -15,8 +15,6 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] -patches = ['libreadline-%(version)s-bugfix.patch'] - builddependencies = [('binutils', '2.27')] dependencies = [('ncurses', '6.0')] -- GitLab From ca1a4fafff488db98e9293a6d4f93b9ee6cde90f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 13:11:17 +0200 Subject: [PATCH 629/818] update extensions in Python 2.7.13 easyconfig, mainly to include numpy 1.12.1 and scipy 0.19.0 --- .../p/Python/Python-2.7.13-intel-2017a.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 31e0d3d932..8d585acc42 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# package versions updated March 6th 2017 +# package versions updated March 30th 2017 exts_list = [ # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, # see https://github.com/pypa/setuptools/issues/980 @@ -42,13 +42,14 @@ exts_list = [ ('nose', '1.3.7', { 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), - ('numpy', '1.12.0', { + ('numpy', '1.12.1', { 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], }), - ('scipy', '0.18.1', { + ('scipy', '0.19.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', }), ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], @@ -90,7 +91,7 @@ exts_list = [ ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), - ('cryptography', '1.7.2', { + ('cryptography', '1.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], }), ('paramiko', '2.1.2', { @@ -111,8 +112,9 @@ exts_list = [ ('mock', '2.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], }), - ('pytz', '2016.10', { + ('pytz', '2017.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'source_tmpl': '%(name)s-%(version)s.zip', }), ('pandas', '0.19.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], -- GitLab From c51102c55e1c7cb3641db800e8c2ac005121464d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 16:39:09 +0200 Subject: [PATCH 630/818] adding easyconfigs: Mesa-17.0.2-intel-2017a.eb, LLVM-4.0.0-intel-2017a.eb, nettle-3.3-intel-2017a.eb, libdrm-2.4.76-intel-2017a.eb, Mako-1.0.6-intel-2017a-Python-2.7.13.eb, libxml2-2.9.4-intel-2017a-Python-2.7.13.eb --- .../l/LLVM/LLVM-4.0.0-intel-2017a.eb | 42 +++++++++++++ .../l/libdrm/libdrm-2.4.76-intel-2017a.eb | 24 +++++++ ...libxml2-2.9.4-intel-2017a-Python-2.7.13.eb | 24 +++++++ .../Mako-1.0.6-intel-2017a-Python-2.7.13.eb | 22 +++++++ .../m/Mesa/Mesa-17.0.2-intel-2017a.eb | 63 +++++++++++++++++++ .../n/nettle/nettle-3.3-intel-2017a.eb | 28 +++++++++ 6 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb new file mode 100644 index 0000000000..5fba0f28fc --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '4.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.13'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb new file mode 100644 index 0000000000..be5c5321ff --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.76' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('X11', '20170129'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8eeb402547 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'libxml2' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), + ('Python', '2.7.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9bae465168 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb new file mode 100644 index 0000000000..70b8bcc2b4 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -0,0 +1,63 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.0.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.6', '-Python-2.7.13'), + ('libxml2', '2.9.4', '-Python-2.7.13'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.3'), + ('libdrm', '2.4.76'), + ('LLVM', '4.0.0'), + ('X11', '20170129'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb new file mode 100644 index 0000000000..d8f9e8fc31 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.3' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' -- GitLab From 65ed10a7fb122fd9bbde169b3234337aedb587c9 Mon Sep 17 00:00:00 2001 From: John Donners Date: Thu, 30 Mar 2017 18:55:11 +0200 Subject: [PATCH 631/818] adding easyconfigs: SCOTCH-6.0.4-intel-2016b.eb --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb index 20bc255b1a..5df84b7224 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' -- GitLab From dd3c0ab7262f61bf0d5187f1ce8307bd4c3afda4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 10:34:22 +0200 Subject: [PATCH 632/818] adding easyconfigs: PGI-17.3-GCC-6.3.0-2.28.eb --- .../p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..fd7e68ba06 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '17.3' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['6eefc42f85e756cbaba76467ed640902'] + +gccver = '6.3.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From 22f66c09d8737d5987422a44069c798e5702ac5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 11:52:19 +0200 Subject: [PATCH 633/818] adding easyconfigs: VTune-2017_update2.eb --- .../easyconfigs/v/VTune/VTune-2017_update2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb new file mode 100644 index 0000000000..5db4d180ba --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb @@ -0,0 +1,15 @@ +name = 'VTune' +version = '2017_update2' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] +checksums = ['1ef91898e107a1da015305def80091e4'] + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From 21c7598a04c602939937779d872a9e59ca0f717c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 15:43:48 +0200 Subject: [PATCH 634/818] add patch to fix build of Mesa 17.0.2 with Intel compilers --- .../easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 3 +++ .../m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch | 14 ++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index 70b8bcc2b4..f2828371e3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -26,6 +26,7 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] builddependencies = [ ('flex', '2.6.3'), @@ -49,6 +50,8 @@ configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm -- configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " +buildopts = 'V=1' + sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch new file mode 100644 index 0000000000..d0aae3dd9c --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch @@ -0,0 +1,14 @@ +strip out '-fp-model source' as a whole, rather than only stripping out '-fp-model' which leads to compilation errors: +"File not found: 'source'" + +author: Ward Poelmans (VUB) +--- mesa-17.0.2/configure.orig 2017-03-31 15:08:32.677119063 +0200 ++++ mesa-17.0.2/configure 2017-03-31 15:09:03.797577051 +0200 +@@ -22317,6 +22317,7 @@ + -e 's/\s\+-O\S*//g' \ + -e 's/\s\+-g\S*//g' \ + -e 's/-fno-rtti\>/-Fno-rtti/g' \ ++ -e 's/\s\+-fp-model \S*//g' \ + -e 's/\s\+-f\S*//g' \ + -e 's/-Fno-rtti\>/-fno-rtti/g' \ + -e 's/^ //' -- GitLab From d9dad61ddaf59e678a9abf97cc7fa9ee16318a9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:28:15 +0200 Subject: [PATCH 635/818] adding easyconfigs: scp-0.10.2-intel-2016b-Python-2.7.12.eb --- .../scp-0.10.2-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1372c5db1e --- /dev/null +++ b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'scp' +version = '0.10.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jbardin/scp.py' +description = """The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From f0df52802c6a87777ca2ca60a7ceff6f977cb419 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:28:41 +0200 Subject: [PATCH 636/818] adding easyconfigs: Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb --- ...Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..c0dc9e45f8 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 77ccc1df9abe43202a2a677829df4cda59bf6b04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:34:12 +0200 Subject: [PATCH 637/818] {data}[intel/2017a] GDAL v2.1.3 + updated deps --- .../GDAL-2.1.3-intel-2017a-Python-2.7.13.eb | 48 +++++++++++++++++++ .../GDAL-2.1.3_fix-uchar-definition.patch | 9 ++++ .../GEOS-3.6.1-intel-2017a-Python-2.7.13.eb | 28 +++++++++++ .../l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 33 +++++++++++++ .../libjpeg-turbo-1.5.1-intel-2017a.eb | 30 ++++++++++++ .../l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb | 29 +++++++++++ .../n/NASM/NASM-2.12.02-intel-2017a.eb | 31 ++++++++++++ .../p/PCRE/PCRE-8.40-intel-2017a.eb | 18 +++++++ .../SWIG-3.0.12-intel-2017a-Python-2.7.13.eb | 20 ++++++++ 9 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..07385fe881 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '2.0.12'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch new file mode 100644 index 0000000000..c70a977531 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch @@ -0,0 +1,9 @@ +--- gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h.orig 2017-03-31 17:06:52.996122910 +0200 ++++ gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h 2017-03-31 17:07:06.356370202 +0200 +@@ -34,4 +34,6 @@ + + jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode); + ++#define uchar unsigned char ++ + #endif diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4483d7a5d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.13')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb new file mode 100644 index 0000000000..9087c14aa4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.7' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb new file mode 100644 index 0000000000..921c5c073d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.1' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.12.02'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..85ea50b710 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.29' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb new file mode 100644 index 0000000000..a4d8935beb --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb new file mode 100644 index 0000000000..b2df6c9ad9 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b90543199e --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PCRE', '8.40'), +] + +moduleclass = 'devel' -- GitLab From bbf0a5bf2bdef4672f51a6750df57ef02ed6bb41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:51:28 +0200 Subject: [PATCH 638/818] adding easyconfigs: LIBSVM-3.22-intel-2016b.eb --- .../l/LIBSVM/LIBSVM-3.22-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb new file mode 100644 index 0000000000..26b2999f95 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.22' + +homepage = 'http://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Qt', '4.8.7')] + +buildopts = ' && cd svm-toy/qt && make MOC=$EBROOTQT/bin/moc ' +buildopts += 'CFLAGS="$CFLAGS -I$EBROOTQT/include -I$EBROOTQT/include/QtGui -lQtGui -lQtCore" && cd -' + +files_to_copy = [(['svm-*'], 'bin'), 'tools'] + +sanity_check_paths = { + 'files': ['bin/svm-%s' % x for x in ['predict', 'scale', 'train']] + ['bin/svm-toy/qt/svm-toy'], + 'dirs': ['bin/svm-toy', 'tools'], +} + +modextrapaths = { + 'PATH': ['bin', 'bin/svm-toy/qt'], +} + +moduleclass = 'lib' -- GitLab From e9b30261c84e53d6c1d33de470ad822df6a81c07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:15:56 +0200 Subject: [PATCH 639/818] consistently add zlib as dependency in SCOTCH easyconfigs --- .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb | 4 ++++ .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb | 4 ++++ 17 files changed, 68 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb index f7e1fa75af..fb8bdd5fe8 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/28978/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb index 63e54d60a9..a840cb128c 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb @@ -12,4 +12,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/28978/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb index adc2bceafc..36e2a02cae 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb index 8e693c1ca4..b9f3cfb699 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb index b0d4836a13..60cfca1ccb 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb index b9f29b45c5..1a0f934621 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb index 89020e5a6b..4e6810fc24 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb index f4c56ce013..68499c20c9 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34099/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index f5bdd9828b..8e49ec9738 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb index 3f65d37408..6646f63b1d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb index 431d04e9df..6627e15ad7 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb index 9fb7233435..e19c44686d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb index b61aa3728e..4bbf975f93 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb index a98a4841f7..173ec5abc6 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb index ba1a0a43d1..a9f67fc882 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb @@ -12,4 +12,8 @@ toolchainopts = {'pic': True, 'i8': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb index 34df491afd..5f4f35c9c0 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb index a90bb75fa5..30e51cb632 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' -- GitLab From e11ecadb7b25a413b83103555ebe21477c841adb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:40:48 +0200 Subject: [PATCH 640/818] adding easyconfigs: cairo-1.14.8-intel-2017a.eb, pixman-0.34.0-GCCcore-6.3.0.eb, GLib-2.52.0-intel-2017a.eb --- .../c/cairo/cairo-1.14.8-intel-2017a.eb | 43 +++++++++++++++++++ .../g/GLib/GLib-2.52.0-intel-2017a.eb | 34 +++++++++++++++ .../p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb new file mode 100644 index 0000000000..6f9eb993e3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.8' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libpng', '1.6.29'), + ('freetype', '2.7.1'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('X11', '20170129'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb new file mode 100644 index 0000000000..dcffcd7dec --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.52.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), +] + +builddependencies = [('Python', '2.7.13')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..185ce92b1d --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 8cea6ea8a6ecbc4dd325a0acdce97bd43aba31af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:41:22 +0200 Subject: [PATCH 641/818] adding easyconfigs: ED2-20170201-intel-2017a-serial.eb --- .../e/ED2/ED2-20170201-intel-2017a-serial.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb new file mode 100644 index 0000000000..0ba1a5a27b --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' +versionsuffix = '-serial' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' PAR_DEFS='' " +buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' + +files_to_copy = [(['ED/build/ed_2.1-opt'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ed_2.1-opt'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From 7040ded550b1739b2a37c1ce8193dcb5c9509991 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 19:03:15 +0200 Subject: [PATCH 642/818] adding easyconfigs: R-3.3.3-intel-2017a-X11-20170129.eb, libGLU-9.0.0-intel-2017a.eb, Tk-8.6.6-intel-2017a.eb, PROJ-4.9.3-intel-2017a.eb --- .../l/libGLU/libGLU-9.0.0-intel-2017a.eb | 24 + .../p/PROJ/PROJ-4.9.3-intel-2017a.eb | 30 ++ .../r/R/R-3.3.3-intel-2017a-X11-20170129.eb | 509 ++++++++++++++++++ .../easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb | 27 + 4 files changed, 590 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb new file mode 100644 index 0000000000..7dff238507 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '17.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb new file mode 100644 index 0000000000..07a9a99e42 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb new file mode 100644 index 0000000000..e0614dfdd9 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb @@ -0,0 +1,509 @@ +name = 'R' +version = '3.3.3' +x11ver = '20170129' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.8'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.17.0'), + ('PCRE', '8.40'), + ('libpng', '1.6.29'), # for plotting in R + ('libjpeg-turbo', '1.5.1'), # for plottting in R + ('LibTIFF', '4.0.7'), + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6'), # for tcltk + ('Tk', '8.6.6'), # for tcltk + ('cURL', '7.53.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on March 7th 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-6', ext_options), + ('abind', '1.4-5', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.1', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.4', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-10', ext_options), + ('mclust', '5.2.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-5', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.0.5', ext_options), + ('checkmate', '1.8.2', ext_options), + ('Rcpp', '0.12.9', ext_options), + ('cubature', '1.3-6', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.1', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.4-0', ext_options), + ('subplex', '1.2-2', ext_options), + ('stringi', '1.1.2', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.2.0', ext_options), + ('evaluate', '0.10', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.9-4', ext_options), + ('plotrix', '3.6-4', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-38', ext_options), + ('SparseM', '1.76', ext_options), + ('tripack', '1.3-8', ext_options), + ('irace', '2.1', ext_options), + ('rJava', '0.9-8', ext_options), + ('lattice', '0.20-34', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-28', ext_options), + ('Matrix', '1.2-8', ext_options), + ('png', '0.1-7', ext_options), + ('RcppArmadillo', '0.7.700.0.0', ext_options), + ('plyr', '1.8.4', ext_options), + ('pROC', '1.9.1', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.11', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-2', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-37', ext_options), + ('pls', '2.6-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-8', ext_options), + ('nnet', '7.3-12', ext_options), + ('nlme', '3.1-131', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.9.0', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.29', ext_options), + ('mgcv', '1.8-17', ext_options), + ('colorspace', '1.3-2', ext_options), + ('robustbase', '0.92-7', ext_options), + ('sp', '1.2-4', ext_options), + ('zoo', '1.7-14', ext_options), + ('lmtest', '0.9-35', ext_options), + ('vcd', '1.4-3', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.40-1', ext_options), + ('mice', '2.30', ext_options), + ('urca', '1.3-0', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.22', ext_options), + ('akima', '0.6-2', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-18', ext_options), + ('mixtools', '1.1.0', ext_options), + ('cluster', '2.0.5', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.19-1', ext_options), + ('codetools', '0.2-15', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.6', ext_options), + ('foreign', '0.8-67', ext_options), + ('gam', '1.14', ext_options), + ('gamlss.data', '5.0-0', ext_options), + ('gamlss.dist', '5.0-0', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-1', ext_options), + ('quantmod', '0.4-7', ext_options), + ('mnormt', '1.5-5', ext_options), + ('mvtnorm', '1.0-6', ext_options), + ('pcaPP', '1.9-61', ext_options), + ('numDeriv', '2016.8-1', ext_options), + ('lava', '1.4.7', ext_options), + ('prodlim', '1.6.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('memoise', '1.0.0', ext_options), + ('plogr', '0.1-1', ext_options), + ('RSQLite', '1.1-2', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-4', ext_options), + ('sfsmisc', '1.1-0', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-3', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-2', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.14', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-38', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.1', ext_options), + ('R.oo', '1.21.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.5.0', ext_options), + ('R.matlab', '3.6.1', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.4.1', ext_options), + ('reshape2', '1.4.2', ext_options), + ('gtable', '0.2.0', ext_options), + ('munsell', '0.4.3', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.4.1', ext_options), + ('proto', '1.0.0', ext_options), + ('lazyeval', '0.2.0', ext_options), + ('assertthat', '0.1', ext_options), + ('tibble', '1.2', ext_options), + ('ggplot2', '2.2.1', ext_options), + ('gridExtra', '2.2.1', ext_options), + ('chron', '2.3-50', ext_options), + ('data.table', '1.10.4', ext_options), + ('viridis', '0.3.4', ext_options), + ('yaml', '2.1.14', ext_options), + ('jsonlite', '1.3', ext_options), + ('htmltools', '0.3.5', ext_options), + ('htmlwidgets', '0.8', ext_options), + ('knitr', '1.15.1', ext_options), + ('htmlTable', '1.9', ext_options), + ('Hmisc', '4.0-2', ext_options), + ('fastcluster', '1.1.22', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.1.2', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '4.1', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '3.0.1', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.2.0', ext_options), + ('rjson', '0.2.15', ext_options), + ('sourcetools', '0.1.5', ext_options), + ('shiny', '1.0.0', ext_options), + ('seqinr', '3.3-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-12', ext_options), + ('gmodels', '2.16.2', ext_options), + ('expm', '0.999-1', ext_options), + ('spdep', '0.6-11', ext_options), + ('dplyr', '0.5.0', ext_options), + ('vegan', '2.4-2', ext_options), + ('adegenet', '2.0.1', ext_options), + ('prettyunits', '1.0.2', ext_options), + ('progress', '1.1.2', ext_options), + ('rncl', '0.8.2', ext_options), + ('XML', '3.98-1.5', ext_options), + ('crayon', '1.3.2', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '1.0.2', ext_options), + ('rprojroot', '1.2', ext_options), + ('rmarkdown', '1.3', ext_options), + ('curl', '2.3', ext_options), + ('openssl', '0.9.6', ext_options), + ('httr', '1.2.1', ext_options), + ('reshape', '0.8.6', ext_options), + ('xml2', '1.1.1', ext_options), + ('bold', '0.4.0', ext_options), + ('triebeard', '0.3.0', ext_options), + ('urltools', '1.6.0', ext_options), + ('httpcode', '0.2.0', ext_options), + ('crul', '0.3.0', ext_options), + ('rredlist', '0.3.0', ext_options), + ('rentrez', '1.0.4', ext_options), + ('rotl', '3.0.3', ext_options), + ('solrium', '0.4.0', ext_options), + ('ritis', '0.5.4', ext_options), + ('worrms', '0.1.0', ext_options), + ('natserv', '0.1.4', ext_options), + ('taxize', '0.8.4', ext_options), + ('tidyr', '0.6.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.7', ext_options), + ('phylobase', '0.8.2', ext_options), + ('adephylo', '1.1-10', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.19', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-8', ext_options), + ('dismo', '1.1-4', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.4', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.10', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-5', ext_options), + ('rgl', '0.98.1', ext_options), + ('labdsv', '1.8-0', ext_options), + ('stabs', '0.6-2', ext_options), + ('modeltools', '0.2-21', ext_options), + ('strucchange', '1.5-1', ext_options), + ('TH.data', '1.0-8', ext_options), + ('multcomp', '1.4-6', ext_options), + ('coin', '1.1-3', ext_options), + ('party', '1.2-2', ext_options), + ('mboost', '2.7-0', ext_options), + ('msm', '1.6.4', ext_options), + ('nor1mix', '1.2-2', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-9', ext_options), + ('polspline', '1.1.12', ext_options), + ('rms', '5.1-0', ext_options), + ('RWekajars', '3.9.1-1', ext_options), + ('RWeka', '0.4-31', ext_options), + ('slam', '0.1-40', ext_options), + ('tm', '0.7-1', ext_options), + ('TraMineR', '1.8-13', ext_options), + ('chemometrics', '1.4.1', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-6', ext_options), + ('statmod', '1.4.29', ext_options), + ('miscTools', '0.6-22', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.3.2', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.3.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.51.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '3.0', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-12', ext_options), + ('pbkrtest', '0.4-6', ext_options), + ('car', '2.1-4', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.35', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.10', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '3.2', ext_options), + ('RGCCA', '2.1', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.0', ext_options), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-1', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.5-6', ext_options), + ('goftest', '1.0-4', ext_options), + ('spatstat', '1.49-0', ext_options), + ('rgdal', '1.2-5', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.9.9', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-1', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-21', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-73', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.10', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.0', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.18.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.12.0', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', ext_options), + ('ks', '1.10.5', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.4.2', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.6.12', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '1.0.3', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('DiagrammeR', '0.9.0', ext_options), + ('sem', '3.1-8', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.1.1', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('imager', '0.31', ext_options), +] + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb new file mode 100644 index 0000000000..325e35acc9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('X11', '20170129'), + ('Tcl', version), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2d73e37dd1ce05ab3f76e27bbe6c7972f3ff8f4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 19:03:49 +0200 Subject: [PATCH 643/818] add util-linux as dependency to GLib --- .../g/GLib/GLib-2.52.0-intel-2017a.eb | 1 + .../util-linux-2.29.2-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb index dcffcd7dec..6b20efcba1 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -17,6 +17,7 @@ dependencies = [ ('gettext', '0.19.8.1'), ('libxml2', '2.9.4'), ('PCRE', '8.40'), + ('util-linux', '2.29.2'), ] builddependencies = [('Python', '2.7.13')] diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb new file mode 100644 index 0000000000..3495ebee0c --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.29.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 98be1ce1add0f4ccea0920abe523f5a7d3182fa8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 20:29:25 +0200 Subject: [PATCH 644/818] adding easyconfigs: X11-20170314-GCCcore-6.3.0.eb, fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb, freetype-2.7.2-GCCcore-6.3.0.eb --- ...fig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb | 27 ++++ .../freetype/freetype-2.7.2-GCCcore-6.3.0.eb | 29 ++++ .../x/X11/X11-20170314-GCCcore-6.3.0.eb | 135 ++++++++++++++++++ 3 files changed, 191 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb new file mode 100644 index 0000000000..cc99c8e530 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' +freetype_ver = '2.7.2' +versionsuffix = '-freetype-%s' % freetype_ver + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', freetype_ver), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..6f9485b3f0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..28c4d48e99 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -0,0 +1,135 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20170314' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.12.1', '-freetype-2.7.2'), + ('zlib', '1.2.11'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.1'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.1', { # 2017-01-29 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.4', common_specs), # 2017-03-14 + ('bigreqsproto', '1.1.2', common_specs), # 2012-03-23 + ('compositeproto', '0.4.2', common_specs), # 2010-10-30 + ('damageproto', '1.2.1', common_specs), # 2010-10-30 + ('dmxproto', '2.3.1', common_specs), # 2011-01-06 + ('dri2proto', '2.8', common_specs), # 2012-07-11 + ('dri3proto', '1.0', common_specs), # 2013-11-01 + ('fixesproto', '5.0', common_specs), # 2011-03-08 + ('fontsproto', '2.1.3', common_specs), # 2014-04-14 + ('glproto', '1.4.17', common_specs), # 2013-12-10 + ('inputproto', '2.3.2', common_specs), # 2016-04-04 + ('kbproto', '1.0.7', common_specs), # 2015-05-01 + ('presentproto', '1.1', common_specs), # 2017-01-26 + ('randrproto', '1.5.0', common_specs), # 2015-05-17 + ('recordproto', '1.14.2', common_specs), # 2012-03-23 + ('renderproto', '0.11.1', common_specs), # 2010-08-10 + ('resourceproto', '1.2.0', common_specs), # 2011-05-28 + ('scrnsaverproto', '1.2.2', common_specs), # 2012-03-23 + ('videoproto', '2.3.3', common_specs), # 2016-03-11 + ('xcmiscproto', '1.2.2', common_specs), # 2012-03-23 + ('xextproto', '7.3.0', common_specs), # 2013-12-27 + ('xf86bigfontproto', '1.2.0', common_specs), # 2009-08-27 + ('xf86dgaproto', '2.1', common_specs), # 2009-10-01 + ('xf86driproto', '2.1.1', common_specs), # 2011-01-06 + ('xf86vidmodeproto', '2.3.1', common_specs), # 2011-01-06 + ('xineramaproto', '1.2.1', common_specs), # 2011-01-06 + ('xproto', '7.0.31', common_specs), # 2016-09-23 + ('libXau', '1.0.8', common_specs), # 2013-05-24 + ('libXdmcp', '1.1.2', common_specs), # 2015-03-21 + ('xcb-proto', '1.12', common_specs), # 2016-05-18 + ('libxcb', '1.12', common_specs), # 2016-05-18 + ('xtrans', '1.3.5', common_specs), # 2014-09-22 + ('libxkbcommon', '0.7.1', { # 2017-01-18 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.5', common_specs), # 2017-02-26 + ('libXext', '1.3.3', common_specs), # 2014-07-24 + ('libFS', '1.0.7', common_specs), # 2015-05-01 + ('libICE', '1.0.9', common_specs), # 2014-06-07 + ('libSM', '1.2.2', common_specs), # 2013-09-08 + ('libXScrnSaver', '1.2.2', common_specs), # 2012-03-08 + ('libXt', '1.1.5', common_specs), # 2015-05-01 + ('libXmu', '1.1.2', common_specs), # 2013-09-08 + ('libXpm', '3.5.12', common_specs), # 2016-12-15 + ('libXaw', '1.0.13', common_specs), # 2015-05-01 + ('libXfixes', '5.0.3', common_specs), # 2016-10-04 + ('libXcomposite', '0.4.4', common_specs), # 2013-01-03 + ('libXrender', '0.9.10', common_specs), # 2016-10-04 + ('libXcursor', '1.1.14', common_specs), # 2013-05-30 + ('libXdamage', '1.1.4', common_specs), # 2013-01-03 + ('libfontenc', '1.1.3', common_specs), # 2015-05-01 + ('libXfont', '1.5.2', common_specs), # 2016-08-31 + ('libXfont2', '2.0.1', common_specs), # 2015-12-11 + ('libXft', '2.3.2', common_specs), # 2014-06-06 + ('libXi', '1.7.9', common_specs), # 2017-01-23 + ('libXinerama', '1.1.3', common_specs), # 2013-05-31 + ('libXrandr', '1.5.1', common_specs), # 2016-10-04 + ('libXres', '1.0.7', common_specs), # 2013-05-31 + ('libXtst', '1.2.3', common_specs), # 2016-10-04 + ('libXv', '1.0.11', common_specs), # 2016-10-04 + ('libXvMC', '1.0.10', common_specs), # 2016-10-04 + ('libXxf86dga', '1.1.4', common_specs), # 2013-05-31 + ('libXxf86vm', '1.1.4', common_specs), # 2015-02-24 + ('libdmx', '1.1.3', common_specs), # 2013-05-28 + ('libpciaccess', '0.13.4', common_specs), # 2015-05-01 + ('libxkbfile', '1.0.9', common_specs), # 2015-05-01 + ('libxshmfence', '1.2', common_specs), # 2015-01-02 + ('xcb-util', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-image', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-keysyms', '0.4.0', common_specs), # 2014-10-01 + ('xcb-util-renderutil', '0.3.9', common_specs), # 2014-06-13 + ('xcb-util-wm', '0.4.1', common_specs), # 2014-02-19 + ('xcb-util-cursor', '0.1.3', common_specs), # 2016-05-12 +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 42b1274584aa7936846cd2f34cfd71df6a72f79c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:06:20 +0200 Subject: [PATCH 645/818] no freetype 2.7.2 yet, change versionsuffix to -libpng-1.6.29 --- ....eb => fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb} | 5 ++--- ...3.0.eb => freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb} | 6 ++++-- easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb | 3 ++- 3 files changed, 8 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/fontconfig/{fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb => fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb} (86%) rename easybuild/easyconfigs/f/freetype/{freetype-2.7.2-GCCcore-6.3.0.eb => freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb} (89%) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb similarity index 86% rename from easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb rename to easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index cc99c8e530..b9da643ed4 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -2,8 +2,7 @@ easyblock = 'ConfigureMake' name = 'fontconfig' version = '2.12.1' -freetype_ver = '2.7.2' -versionsuffix = '-freetype-%s' % freetype_ver +versionsuffix = '-libpng-1.6.29' homepage = 'http://www.freedesktop.org/software/fontconfig' description = """Fontconfig is a library designed to provide system-wide font configuration, customization and @@ -16,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.2.0'), - ('freetype', freetype_ver), + ('freetype', '2.7.1', versionsuffix), ] # use same binutils version that was used when building GCCcore toolchain diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb similarity index 89% rename from easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index 6f9485b3f0..1b0dc16aba 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -1,5 +1,7 @@ name = 'freetype' -version = '2.7.2' +version = '2.7.1' +libpng_ver = '1.6.29' +versionsuffix = '-libpng-%s' % libpng_ver homepage = 'http://freetype.org' description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and @@ -13,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('bzip2', '1.0.6'), - ('libpng', '1.6.29'), + ('libpng', libpng_ver), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb index 28c4d48e99..dc3461eb7f 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -18,7 +18,8 @@ source_urls = [ dependencies = [ ('bzip2', '1.0.6'), - ('fontconfig', '2.12.1', '-freetype-2.7.2'), + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ('zlib', '1.2.11'), ] builddependencies = [ -- GitLab From 6c8b36edb3ad6280a15cc4cfc13bfabebeb5710c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:07:15 +0200 Subject: [PATCH 646/818] bump X11 to version 20170314 in Mesa 17.0.2 easyconfig --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb index be5c5321ff..a8a5a109c8 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2017a'} dependencies = [ - ('X11', '20170129'), + ('X11', '20170314'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index f2828371e3..8bb12d31a3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -42,7 +42,7 @@ dependencies = [ ('nettle', '3.3'), ('libdrm', '2.4.76'), ('LLVM', '4.0.0'), - ('X11', '20170129'), + ('X11', '20170314'), ] # GLU is not part anymore of Mesa package! -- GitLab From 20ef59bf583714a6cf3719bdffc7e2978ad23024 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:10:07 +0200 Subject: [PATCH 647/818] bump X11 dep version in cairo 1.14.8 easyconfig --- easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb index 6f9eb993e3..6be8104cc5 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -21,7 +21,7 @@ dependencies = [ ('pixman', '0.34.0'), ('expat', '2.2.0'), ('GLib', '2.52.0'), - ('X11', '20170129'), + ('X11', '20170314'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -- GitLab From 22f35fb732e032fa70bcedfe12fcf01bffec2f89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:11:57 +0200 Subject: [PATCH 648/818] bump X11 deps to 20170314 --- ...017a-X11-20170129.eb => R-3.3.3-intel-2017a-X11-20170314.eb} | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/R/{R-3.3.3-intel-2017a-X11-20170129.eb => R-3.3.3-intel-2017a-X11-20170314.eb} (99%) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb similarity index 99% rename from easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb rename to easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index e0614dfdd9..6892093317 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -1,6 +1,6 @@ name = 'R' version = '3.3.3' -x11ver = '20170129' +x11ver = '20170314' versionsuffix = '-X11-%s' % x11ver homepage = 'http://www.r-project.org/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb index 325e35acc9..a01bad3db9 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -15,7 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] dependencies = [ - ('X11', '20170129'), + ('X11', '20170314'), ('Tcl', version), ('zlib', '1.2.11'), ] -- GitLab From 113e1afec23069c309e9b805b51809af27f54de1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:47:22 +0200 Subject: [PATCH 649/818] fix freetype dep in cairo 1.14.8 easyconfig --- easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb index 6be8104cc5..872e069d81 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -17,7 +17,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.11'), ('libpng', '1.6.29'), - ('freetype', '2.7.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ('pixman', '0.34.0'), ('expat', '2.2.0'), ('GLib', '2.52.0'), -- GitLab From ad7470594727b093fefd925cf9cf6b40ad5e802f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 22:32:51 +0200 Subject: [PATCH 650/818] include patches for R v3.3.3 extensions to fix compilation with Intel compilers --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 6892093317..75250e8769 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -79,7 +79,7 @@ exts_list = [ ('Rmpi', '0.6-6', ext_options), ('abind', '1.4-5', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('bit', '1.1-12', ext_options), ('filehash', '2.3', ext_options), ('ff', '2.2-13', ext_options), @@ -324,7 +324,7 @@ exts_list = [ ('adephylo', '1.1-10', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.19', ext_options), + ('bigmemory', '4.5.19', dict(ext_options.items() + [('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), ('raster', '2.5-8', ext_options), @@ -407,7 +407,7 @@ exts_list = [ ('VennDiagram', '1.6.17', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), - ('forecast', '8.0', ext_options), + ('forecast', '8.0', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.3', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', ext_options), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), @@ -483,7 +483,7 @@ exts_list = [ ('network', '1.13.0', ext_options), ('statnet.common', '3.3.0', ext_options), ('sna', '2.4', ext_options), - ('glasso', '1.8', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), ('huge', '1.2.7', ext_options), ('d3Network', '0.5.2.1', ext_options), ('ggm', '2.3', ext_options), -- GitLab From d845dddaa77015db0f0b283f52559461647d5738 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 12:02:44 +0200 Subject: [PATCH 651/818] adding easyconfigs: Spack-0.10.0.eb --- easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb new file mode 100644 index 0000000000..3a97b911b1 --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Spack' +version = '0.10.0' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/LLNL/spack/archive/'] +sources = ['v%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' -- GitLab From 5c10b74a26b8517f3c9462ce128ef51f9867bf82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 21:19:46 +0200 Subject: [PATCH 652/818] fix patch for multicool-0.1-10 extension in R 3.3.3 easyconfig --- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 75250e8769..eb14dda6a0 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-10_icpc-wd308.patch', 1)])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch new file mode 100644 index 0000000000..a86f23d77d --- /dev/null +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -0,0 +1,7 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 ++++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 +@@ -0,0 +1,2 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 23693fca6ad76a06c641d3110ef58445491d73f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 21:32:43 +0200 Subject: [PATCH 653/818] make sure multicool patch level can be derived --- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index eb14dda6a0..06a44541b2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-10_icpc-wd308.patch', 1)])])), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', ['multicool-0.1-10_icpc-wd308.patch'])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch index a86f23d77d..660089c7d5 100644 --- a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -1,5 +1,12 @@ add -wd308 compiler option to avoid compiler warning #308 being treated as an error author: Kenneth Hoste (HPC-UGent) +--- multicool/MD5.orig 2017-04-01 21:30:37.105382230 +0200 ++++ multicool/MD5 2017-04-01 21:30:30.095337987 +0200 +@@ -20,3 +20,4 @@ + b18b7e9e5912cf1014aa2c2fa8e86047 *src/compositions.cpp + 994ea793adf2455b973554d9b8dacd99 *src/multicool.cpp + 8e6ea24037e92ec9c30f699f4e3f9b8a *src/multinomial.h ++b1d3a4d02405fe08c7983c479bc27f13 */src/Makevars --- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 +++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 @@ -0,0 +1,2 @@ -- GitLab From 1db6d2bc186632ac3e477de75e3620300e4364e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Apr 2017 09:43:12 +0200 Subject: [PATCH 654/818] add patch for imager extension in R 3.3.3 easyconfig --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../r/R/imager-0.3_fix-icpc-bool-cast.patch | 259 ++++++++++++++++++ 2 files changed, 260 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 06a44541b2..01ebe2e855 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -502,7 +502,7 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', ext_options), + ('imager', '0.31', dict(ext_options.items() + [('patches', ['imager-0.3_fix-icpc-bool-cast.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch new file mode 100644 index 0000000000..8d994cb858 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch @@ -0,0 +1,259 @@ +fix Intel compilation errors, partially based on https://github.com/dtschump/CImg/commit/d66a4e7f1b13594a572c22160c20e2bd3f231f6c +author: Kenneth Hoste (HPC-UGent) +--- imager/inst/include/CImg.h.orig 2016-08-31 16:30:10.000000000 +0200 ++++ imager/inst/include/CImg.h 2017-04-01 22:43:25.292695440 +0200 +@@ -17988,7 +17988,7 @@ + unsigned int ind = (unsigned int)mp.opcode[2]; + if (ind!=~0U) ind = (unsigned int)cimg::mod((int)_mp_arg(2),mp.listin.width()); + CImg &img = ind==~0U?mp.imgout:mp.listout[ind]; +- if (img) { ++ if ((bool)img) { + if (mp.opcode[12]!=(ulongT)-1) { + const CImg M(&_mp_arg(12) + 1,dx,dy,dz,(unsigned int)mp.opcode[13],true); + img.draw_image(x,y,z,c,S,M,opacity,(float)_mp_arg(14)); +@@ -18107,10 +18107,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18184,10 +18184,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18257,10 +18257,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18317,10 +18317,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img(ind,cimg::mod(off,whds)); ++ if ((bool)img) return (double)img(ind,cimg::mod(off,whds)); + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18590,7 +18590,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -18662,7 +18662,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -19579,7 +19579,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -19648,7 +19648,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -25664,14 +25664,15 @@ + x0 = ((int)xc%width()) - width(), + y0 = ((int)yc%height()) - height(), + z0 = ((int)zc%depth()) - depth(), +- c0 = ((int)cc%spectrum()) - spectrum(); ++ c0 = ((int)cc%spectrum()) - spectrum(), ++ dx = width(), dy = height(), dz = depth(), dc = spectrum(); + #ifdef cimg_use_openmp + #pragma omp parallel for collapse(3) if (res.size()>=65536) + #endif +- for (int c = c0; c<(int)sc; c+=spectrum()) +- for (int z = z0; z<(int)sz; z+=depth()) +- for (int y = y0; y<(int)sy; y+=height()) +- for (int x = x0; x<(int)sx; x+=width()) ++ for (int c = c0; c<(int)sc; c+=dc) ++ for (int z = z0; z<(int)sz; z+=dz) ++ for (int y = y0; y<(int)sy; y+=dy) ++ for (int x = x0; x<(int)sx; x+=dx) + res.draw_image(x,y,z,c,*this); + } break; + case 1 : { // Neumann boundary. +@@ -47059,7 +47060,7 @@ + const IplImage *img = 0; + for (unsigned int i = 0; iwidthStep - 3*img->width); + assign(img->width,img->height,1,3); + const unsigned char* ptrs = (unsigned char*)img->imageData; +@@ -52636,7 +52637,7 @@ + case 'x' : { // Along the X-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx+=img._width; + dy = cimg::max(dy,img._height); + dz = cimg::max(dz,img._depth); +@@ -52646,7 +52647,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image(pos, ++ if ((bool)img) res.draw_image(pos, + (int)(align*(dy - img._height)), + (int)(align*(dz - img._depth)), + (int)(align*(dc - img._spectrum)), +@@ -52657,7 +52658,7 @@ + case 'y' : { // Along the Y-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy+=img._height; + dz = cimg::max(dz,img._depth); +@@ -52667,7 +52668,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + pos, + (int)(align*(dz - img._depth)), + (int)(align*(dc - img._spectrum)), +@@ -52678,7 +52679,7 @@ + case 'z' : { // Along the Z-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy = cimg::max(dy,img._height); + dz+=img._depth; +@@ -52688,7 +52689,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + (int)(align*(dy - img._height)), + pos, + (int)(align*(dc - img._spectrum)), +@@ -52699,7 +52700,7 @@ + default : { // Along the C-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy = cimg::max(dy,img._height); + dz = cimg::max(dz,img._depth); +@@ -52709,7 +52710,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + (int)(align*(dy - img._height)), + (int)(align*(dz - img._depth)), + pos, +@@ -53957,7 +53958,7 @@ + CImg img; + try { img.load_pnm(filename_tmp2); } + catch (CImgException&) { stop_flag = true; } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + } + cimg::exception_mode(omode); + if (is_empty()) +@@ -54033,7 +54034,7 @@ + CImg img; + try { img.load_png(filename_tmp2); } + catch (CImgException&) { } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + else { // Try to read animated gif. + unsigned int i = 0; + for (bool stop_flag = false; !stop_flag; ++i) { +@@ -54042,7 +54043,7 @@ + CImg img; + try { img.load_png(filename_tmp2); } + catch (CImgException&) { stop_flag = true; } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + } + } + cimg::exception_mode(omode); +--- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 ++++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 +@@ -1,4 +1,5 @@ + + PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 + PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +--- imager/MD5.orig 2016-09-12 15:08:55.000000000 +0200 ++++ imager/MD5 2017-04-01 22:44:16.943021224 +0200 +@@ -31,7 +31,7 @@ + 05e04a3bc5a858c40e001cc65b853dfc *inst/extdata/Leonardo_Birds.jpg + e1328ba2c55d5a72eb77e283c9630b90 *inst/extdata/parrots.png + daa5b7e30235689ad0444df37c88b7ff *inst/extdata/tennis_sif.mpeg +-00de9e6b4c2066d28d7f8d9e251915cd *inst/include/CImg.h ++ea9acc61a3dd73452639c570af543d29 *inst/include/CImg.h + 034a9e8aab9e05094fd31ce9ea3bbae2 *inst/include/imager.h + 0c8aae8db902f96a8f8e323043eb1418 *inst/include/wrappers.h + be39be77874a0181ecd47b1a7a9af5dd *man/FFT.Rd +@@ -140,7 +140,7 @@ + a680472a2ef1eda48c1a9b90488543b5 *man/vanvliet.Rd + 08193940e20b440f614e4c7a2dbf82fb *man/warp.Rd + 429b25a38f282c30d5d178ad9efc3b1f *man/watershed.Rd +-ab8f97aa6f15c67d1029e3eb5091853d *src/Makevars.in ++802ecbe76012c51adf729063804c793a *src/Makevars.in + 5ecf9e8577f31e535dee1c371e75a35f *src/Makevars.win + 78aff3a88c55983a329723eb1174a4ca *src/RcppExports.cpp + 8193f4fecd751c7d310d23b0faacd303 *src/colourspace.cpp -- GitLab From a5f2063b833b5bf00edccfe0167ac1a396850d5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Apr 2017 16:03:04 +0200 Subject: [PATCH 655/818] adding easyconfigs: ClusterShell-1.7.3.eb --- .../c/ClusterShell/ClusterShell-1.7.3.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb new file mode 100644 index 0000000000..7a6d8ed9f6 --- /dev/null +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ClusterShell' +version = '1.7.3' + +homepage = 'http://cea-hpc.github.io/clustershell/' +description = """ClusterShell is an event-driven open source Python library, designed to run local or distant commands + in parallel on server farms or on large Linux clusters.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +options = {'modulename': 'ClusterShell'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/clubak', 'bin/clush', 'bin/nodeset'], + 'dirs': ['lib/python%s/site-packages' % pyshortver] +} + +moduleclass = 'tools' -- GitLab From 5663f27a280b6494a5efef3dae1bf526ec75fd1f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 08:13:41 +0100 Subject: [PATCH 656/818] adding easyconfigs: ALLPATHS-LG-52488-foss-2016a.eb --- .../ALLPATHS-LG-52488-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb new file mode 100755 index 0000000000..3ba22f9da5 --- /dev/null +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +# 52488 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ALLPATHS-LG' +version = '52488' + +homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' +description = """ALLPATHS-LG, the new short read genome assembler.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# source is moved over time, hence multiple URLs below +source_urls = [ + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code', + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06', + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06', +] +sources = ['allpathslg-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From a041d36a1b35a350727fee2733daa96baeb39e8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 10:48:18 +0200 Subject: [PATCH 657/818] adding easyconfigs: Inspector-2017_update2.eb --- .../i/Inspector/Inspector-2017_update2.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb new file mode 100644 index 0000000000..9ea21d95ae --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -0,0 +1,17 @@ +name = 'Inspector' +version = '2017_update2' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_%(version)s.tar.gz'] +checksums = ['d85a3bbd699b0fc77967fcd5e923ad35'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From b71a103e395e5a84fad3efd2089ffe1748da8238 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 3 Apr 2017 11:05:44 +0200 Subject: [PATCH 658/818] adding easyconfigs: samblaster-0.1.24-goolf-1.7.20.eb --- .../samblaster-0.1.24-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb new file mode 100644 index 0000000000..55c7310c7e --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'samblaster' +version = '0.1.24' + +homepage = 'https://github.com/GregoryFaust/samblaster' +description = """samblaster: a tool to mark duplicates and extract discordant and split reads from sam files""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] +sources = ['v.%(version)s.tar.gz'] + +files_to_copy = [(['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/samblaster'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 33a00c24c74c17fb559dcdb9cb4f6b532f95362a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 11:29:09 +0200 Subject: [PATCH 659/818] adding easyconfigs: ImageMagick-7.0.5-4-intel-2017a.eb, Ghostscript-9.21-intel-2017a.eb, LittleCMS-2.8-intel-2017a.eb --- .../Ghostscript-9.21-intel-2017a.eb | 35 ++++++++++++++++ .../ImageMagick-7.0.5-4-intel-2017a.eb | 42 +++++++++++++++++++ .../l/LittleCMS/LittleCMS-2.8-intel-2017a.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb new file mode 100644 index 0000000000..e055f488f1 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.21' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = ['ghostscript-%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('LibTIFF', '4.0.7'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb new file mode 100644 index 0000000000..b01509be3a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.5-4' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.imagemagick.org/download/releases/'] +checksums = ['473a1e7ae37548eb6fe9cf2b1fb78011'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20170314'), + ('Ghostscript', '9.21'), + ('JasPer', '2.0.12'), + ('libjpeg-turbo', '1.5.1'), + ('LibTIFF', '4.0.7'), + ('LittleCMS', '2.8'), +] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb new file mode 100644 index 0000000000..338a40a66d --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.8' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.5.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' -- GitLab From 674a1c51476cf8e99d35adf0eff04ac75f62cd02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 12:04:18 +0200 Subject: [PATCH 660/818] add PyYAML as dependency for ClusterShell --- .../c/ClusterShell/ClusterShell-1.7.3.eb | 1 + .../easyconfigs/l/libyaml/libyaml-0.1.7.eb | 28 +++++++++++++++++++ easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb | 25 +++++++++++++++++ 3 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb index 7a6d8ed9f6..26131a5764 100644 --- a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('PyYAML', '3.12')] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] options = {'modulename': 'ClusterShell'} diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb new file mode 100644 index 0000000000..44f94ecc3d --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.7' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb new file mode 100644 index 0000000000..8a6937f145 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libyaml', '0.1.7')] +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +options = {'modulename': 'yaml'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': [('lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver)] +} + +moduleclass = 'lib' -- GitLab From 7859c40ad54c1bb3b76ec5037be59eddf796668b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 11:18:29 +0100 Subject: [PATCH 661/818] Remove obsolete FTP paths --- .../easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index 3ba22f9da5..a840c61253 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -19,13 +19,12 @@ version = '52488' homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' description = """ALLPATHS-LG, the new short read genome assembler.""" +# Compilation fails with GCC 5.3 (goss-2016b) toolchain = {'name': 'foss', 'version': '2016a'} # source is moved over time, hence multiple URLs below source_urls = [ 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code', - 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06', - 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06', ] sources = ['allpathslg-%(version)s.tar.gz'] -- GitLab From 36b2bfee952f02ce6b499e5f5b7ba8b5d112b5b7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 11:21:44 +0100 Subject: [PATCH 662/818] Fix typo --- .../easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index a840c61253..0227efebd7 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -19,7 +19,7 @@ version = '52488' homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' description = """ALLPATHS-LG, the new short read genome assembler.""" -# Compilation fails with GCC 5.3 (goss-2016b) +# Compilation fails with GCC 5.3 (foss-2016b) toolchain = {'name': 'foss', 'version': '2016a'} # source is moved over time, hence multiple URLs below -- GitLab From 8c68ce861deb926d89f492e0eaf100c735ef9995 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 17:41:12 +0200 Subject: [PATCH 663/818] adding easyconfigs: deap-0.9.2-intel-2016b-Python-2.7.12.eb --- .../deap-0.9.2-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f639521510 --- /dev/null +++ b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'deap' +version = '0.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deap.readthedocs.org/en/master/' +description = """DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. + It seeks to make algorithms explicit and data structures transparent.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From e28163397a26a71ad0c592cafa5b85b4a7b56c78 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 4 Apr 2017 12:14:05 +0930 Subject: [PATCH 664/818] Support for BioKanga 4.3.4 --- .../b/BioKanga/BioKanga-4.3.4-foss-2015b.eb | 30 +++++++++++++++++++ .../b/BioKanga/BioKanga-4.3.4_configure.patch | 29 ++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb new file mode 100644 index 0000000000..da082e4501 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.4' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['BioKanga-4.3.4_configure.patch'] + +builddependencies = [ + ('Autoconf', '2.69'), + ('Automake', '1.15') +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch new file mode 100644 index 0000000000..a88701ea28 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -0,0 +1,29 @@ +--- ./configure.ac 2017-04-04 11:47:18.067209892 +0930 ++++ ./configure.ac 2017-04-04 11:47:46.719519662 +0930 +@@ -23,11 +23,10 @@ + fasta2dist/Makefile locsw/Makefile quickcount/Makefile csv2feat/Makefile + genalignref2relloci/Makefile genalignloci2core/Makefile maploci2features/Makefile + processcsvfiles/Makefile genalignconf/Makefile Loci2Phylip/Makefile blast2csv/Makefile genrollups/Makefile +- gengoterms/Makefile gengoassoc/Makefile goassoc/Makefile + genWiggle/Makefile gencentroidmetrics/Makefile proccentroids/Makefile DNAseqSitePotential/Makefile SimulateMNase/Makefile + filterreads/Makefile prednucleosomes/Makefile RNAseqSitePotential/Makefile + genDESeq/Makefile fasta2struct/Makefile kangarg/Makefile genultras/Makefile +- LocateROI/Makefile genstructprofile/Makefile genstructstats/Makefile predconfnucs/Makefile gennucstats/Makefile fastafilter/Makefile ++ LocateROI/Makefile genstructprofile/Makefile predconfnucs/Makefile gennucstats/Makefile fastafilter/Makefile + BEDMerge/Makefile BEDFilter/Makefile genElementProfiles/Makefile genzygosity/Makefile genGenomeFromAGP/Makefile genmarkers/Makefile + HammingDist/Makefile genreadsde/Makefile ufilter/Makefile uhamming/Makefile genseqcandidates/Makefile GFFfilter/Makefile loci2dist/Makefile + genNormWiggle/Makefile GTFfilter/Makefile genDiffExpr/Makefile dmpbioseq/Makefile genpseudogenome/Makefile usimdiffexpr/Makefile RNAFragSim/Makefile mergeoverlaps/Makefile +--- Makefile.am 2017-04-04 11:51:40.878045716 +0930 ++++ Makefile.am 2017-04-04 11:51:57.518224861 +0930 +@@ -8,10 +8,9 @@ + genalignref2relloci genalignloci2core maploci2features \ + processcsvfiles genalignconf Loci2Phylip blast2csv genrollups \ + genWiggle proccentroids gencentroidmetrics SimulateMNase predconfnucs \ +- gengoterms gengoassoc goassoc \ + DNAseqSitePotential RNAseqSitePotential prednucleosomes gennucstats \ + uhamming LocateROI genDESeq genGenomeFromAGP kangarg genultras \ +- genstructprofile genstructstats filterreads fasta2struct ufilter genseqcandidates genmarkers GFFfilter \ ++ genstructprofile filterreads fasta2struct ufilter genseqcandidates genmarkers GFFfilter \ + genElementProfiles BEDMerge BEDFilter loci2dist genzygosity genNormWiggle GTFfilter genDiffExpr \ + dmpbioseq genpseudogenome usimdiffexpr genreadsde HammingDist RNAFragSim mergeoverlaps fastafilter \ + kangasr kangar kangahrdx kangade kangas kangapr csv2sqlite biokanga locmarkers PEscaffold SSRdiscovery pacbiokanga -- GitLab From ed49e763dc0bd0d51fe8a687cc1dc6056c9ab11d Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 4 Apr 2017 12:34:08 +0930 Subject: [PATCH 665/818] Added missing easyconfig dependencies for foss-2015b toolchain --- .../a/Autoconf/Autoconf-2.69-foss-2015b.eb | 25 ++++++++++++++ .../a/Automake/Automake-1.15-foss-2015b.eb | 33 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb new file mode 100644 index 0000000000..408f488eca --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb new file mode 100644 index 0000000000..543e7a0ba7 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 2c0bd091e388bc06f25908f60bdaf821e2efeb9b Mon Sep 17 00:00:00 2001 From: Edoardo Di Lorenzo Date: Tue, 4 Apr 2017 09:54:03 +0200 Subject: [PATCH 666/818] adding easyconfigs: Cantera-2.3.0-foss-2016b-Python-2.7.12.eb --- .../Cantera-2.3.0-foss-2016b-Python-2.7.12.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..87566ca1da --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,50 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'Cantera-%(version)s_fix-bug-416.patch', + 'Cantera-%(version)s_fix-test-reprod.patch', +] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('SUNDIALS', '2.7.0'), + ('Eigen', '3.3.2'), + ('fmt', '3.0.1'), + ('googletest', '1.8.0'), +] +builddependencies = [ + ('SCons', '2.5.1', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + common_opts +runtest = 'test ' + common_opts +installopts = 'install ' + common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mixmaster'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' -- GitLab From 504315aa55cf670592a7dfaa04a662012782ee73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 10:03:58 +0200 Subject: [PATCH 667/818] {bio}[intel/2016b] Stampy v1.0.31 w/ Python 2.7.12 --- ...Stampy-1.0.31-intel-2016b-Python-2.7.12.eb | 35 ++++++++++++++++ .../Stampy/Stampy-1.0.31_fix-hardcoding.patch | 40 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1c6a84db5e --- /dev/null +++ b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Stampy' +version = '1.0.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.well.ox.ac.uk/stampy' +description = """Stampy is a package for the mapping of short reads from illumina sequencing machines onto + a reference genome.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +# download via http://www.well.ox.ac.uk/software-download-registration and rename from Stampy-latest.tgz +sources = ['Stampy-%(version)s.tgz'] +checksums = ['512b2da5a952a65d2e6f70220c4641dc'] + +patches = ['Stampy-%(version)s_fix-hardcoding.patch'] + +dependencies = [('Python', '2.7.12')] + +files_to_copy = ['ext', 'maptools.%s' % SHLIB_EXT, 'plugins', 'README.txt', 'Stampy', 'stampy.py'] + +sanity_check_paths = { + 'files': ['maptools.%s' % SHLIB_EXT, 'stampy.py'], + 'dirs': ['ext', 'plugins', 'Stampy'], +} + +modextrapaths = { + # add top-level install path to $PATH and $PYTHONPATH + 'PATH': [''], + 'PYTHONPATH': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch new file mode 100644 index 0000000000..ce59a23011 --- /dev/null +++ b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch @@ -0,0 +1,40 @@ +--- stampy-1.0.31/makefile.orig 2016-12-01 17:28:32.000000000 +0100 ++++ stampy-1.0.31/makefile 2017-04-04 09:59:04.057705404 +0200 +@@ -3,6 +3,10 @@ + # Compiles with gcc 5.4.0 and Apple LLVM version 6.1.0 + # + ++CC?=gcc ++CXX?=g++ ++CFLAGS?=-O2 ++CXXFLAGS?= + SHELL=/bin/bash + python?=python + platform=`uname` +@@ -31,21 +35,21 @@ + + $(bdir)/c/%.o: + mkdir -p $(bdir)/c +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c c/$*.c -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c c/$*.c -o $@ + + $(bdir)/pyx/%.o: + mkdir -p $(bdir)/pyx + ln -s -f `pwd`/pyx/$(ucs)/$*.c pyx/$*.c +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c pyx/$*.c -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c pyx/$*.c -o $@ + + $(bdir)/%.o: +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c ext/readalign/$*.cc -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c ext/readalign/$*.cc -o $@ + + build-stampy: $(objs) + cp -r build/python2.7/* . + @if [ $(platform) = Linux ]; then \ +- g++ `$(python)-config --ldflags` -pthread -shared $(objs) -o maptools.so ; \ ++ $(CXX) `$(python)-config --ldflags` -pthread -shared $(objs) -o maptools.so ; \ + else \ +- g++ `$(python)-config --ldflags` -pthread -dynamiclib $(objs) -o maptools.so ; \ ++ $(CXX) `$(python)-config --ldflags` -pthread -dynamiclib $(objs) -o maptools.so ; \ + fi + -- GitLab From 104319a4179492a63772b13e76cb8d051b248f09 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:23:37 +0200 Subject: [PATCH 668/818] missing dep --- .../s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb new file mode 100644 index 0000000000..21d1aa5067 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.7.0' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.6.2')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' -- GitLab From f37de2420a9c1c3105717e39e765a76951c55205 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:23:57 +0200 Subject: [PATCH 669/818] missing dep --- .../easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb new file mode 100644 index 0000000000..bab8954a19 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.2' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 3be2fdf53413ebf2aa43b7df16ce006bb80cfd60 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:19 +0200 Subject: [PATCH 670/818] missing dep --- .../easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb new file mode 100644 index 0000000000..6faff2689b --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '3.0.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' -- GitLab From bb9e516ef8adbfa25e3e8b9bc65cd1a2118a0e97 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:36 +0200 Subject: [PATCH 671/818] missing dep --- .../googletest/googletest-1.8.0-foss-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb new file mode 100644 index 0000000000..51ca2d0db0 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.8.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's C++ test framework" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgmock.a', 'lib/libgmock_main.a', 'lib/libgtest.a', 'lib/libgtest_main.a'], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' -- GitLab From ce46e440b36dd05543bf1c0982a03360faf138a8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:59 +0200 Subject: [PATCH 672/818] missing dep --- .../SCons-2.5.1-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..40cbf3c559 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From e653637f60899545e584b8abce4485607356e097 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:25:20 +0200 Subject: [PATCH 673/818] missing dep --- .../3to2-1.1.1-foss-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5236c8830e --- /dev/null +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = '3to2' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/3to2' +description = """lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x + into Python version 2.x.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [('Python', '2.7.12')] + +options = {'modulename': 'lib3to2'} + +sanity_check_paths = { + 'files': ['bin/3to2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From ad5231b3ecf0c03a913ffabe6c000a7f969d3399 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 4 Apr 2017 13:10:31 +0200 Subject: [PATCH 674/818] adding easyconfigs: Sambamba-0.6.6.eb --- .../easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb new file mode 100644 index 0000000000..cd17c8d34d --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Sambamba' +version = '0.6.6' + +homepage = 'http://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool (and library), + written in the D programming language, for working with SAM and BAM files. Current functionality + is an important subset of samtools functionality, including view, index, sort, markdup, and depth""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] +sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] + +sanity_check_paths = { + 'files': ['sambamba_v%(version)s'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': "", +} + +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + +moduleclass = 'bio' -- GitLab From 1a436e8b4ff18fd3e7d68944ff2f6a851cd46d02 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 13:16:24 +0200 Subject: [PATCH 675/818] style fixes --- .../s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb index 55c7310c7e..a99c1c0912 100644 --- a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -16,10 +16,11 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] sources = ['v.%(version)s.tar.gz'] -files_to_copy = [(['samblaster'], 'bin/'), - 'README.md', - 'SAMBLASTER_Supplemental.pdf', - 'LICENSE.txt', +files_to_copy = [ + (['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', ] sanity_check_paths = { -- GitLab From e96add50c8edc330c81ed35a3bf500d241a9b126 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 13:41:54 +0200 Subject: [PATCH 676/818] adding easyconfigs: Perl-5.24.1-intel-2017a.eb --- .../p/Perl/Perl-5.24.1-intel-2017a.eb | 893 ++++++++++++++++++ 1 file changed, 893 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb new file mode 100644 index 0000000000..a2c5b790f2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -0,0 +1,893 @@ +name = 'Perl' +version = '5.24.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.38', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.11', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4222', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.26', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.418', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.044', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.42', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', 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'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.132', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 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['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.047', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.49.1', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.9', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.13', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Test::Deep', '1.126', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + }), + 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'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.13', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.25', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.31', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Parse::RecDescent', '1.967014', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.40', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.92', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.42', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.03', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.47', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.14', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KJ/KJALB'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.2004', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9164', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + }), +] + +moduleclass = 'lang' -- GitLab From f47b5a553604438de699f09d452f750f51c4df1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 13:45:47 +0200 Subject: [PATCH 677/818] add comment with info on last update of Perl extensions --- easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index a2c5b790f2..7186e3ec91 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] +# !! order of extensions is important !! +# extensions updated on April 4th 2017 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', -- GitLab From f94439f39c75c014db0eb230041cbeac2d02d0c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2017 14:28:30 +0100 Subject: [PATCH 678/818] adding easyconfigs: matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb --- ...tplotlib-2.0.0-foss-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2f829b0767 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.7'), + ('libpng', '1.6.26'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 3cb81f831d69775ac510480c8dc116e468e78258 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2017 14:54:03 +0100 Subject: [PATCH 679/818] adding easyconfigs: MultiQC-0.9-foss-2016b-Python-2.7.12.eb --- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a7a94c8c8c --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Adam Huffman +# The Francis Crick Institute +easyblock = 'PythonPackage' + +name = 'MultiQC' +version = '0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/ewels/MultiQC/archive'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '2.0.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' -- GitLab From e9dd3eee1b8bf54fae66b954aaf7705665188d6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 18:45:56 +0200 Subject: [PATCH 680/818] update imager extensions to 0.40.1 + add patch to fix compilation with Intel compilers --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 3 +- .../r/R/imager-0.3_fix-icpc-bool-cast.patch | 259 --------------- .../r/R/imager-0.40.1_fix-CImg-icpc.patch | 310 ++++++++++++++++++ 3 files changed, 312 insertions(+), 260 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch create mode 100644 easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 01ebe2e855..7c666ff2ec 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -502,7 +502,8 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', dict(ext_options.items() + [('patches', ['imager-0.3_fix-icpc-bool-cast.patch'])])), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', dict(ext_options.items() + [('patches', ['imager-0.40.1_fix-CImg-icpc.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch deleted file mode 100644 index 8d994cb858..0000000000 --- a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch +++ /dev/null @@ -1,259 +0,0 @@ -fix Intel compilation errors, partially based on https://github.com/dtschump/CImg/commit/d66a4e7f1b13594a572c22160c20e2bd3f231f6c -author: Kenneth Hoste (HPC-UGent) ---- imager/inst/include/CImg.h.orig 2016-08-31 16:30:10.000000000 +0200 -+++ imager/inst/include/CImg.h 2017-04-01 22:43:25.292695440 +0200 -@@ -17988,7 +17988,7 @@ - unsigned int ind = (unsigned int)mp.opcode[2]; - if (ind!=~0U) ind = (unsigned int)cimg::mod((int)_mp_arg(2),mp.listin.width()); - CImg &img = ind==~0U?mp.imgout:mp.listout[ind]; -- if (img) { -+ if ((bool)img) { - if (mp.opcode[12]!=(ulongT)-1) { - const CImg M(&_mp_arg(12) + 1,dx,dy,dz,(unsigned int)mp.opcode[13],true); - img.draw_image(x,y,z,c,S,M,opacity,(float)_mp_arg(14)); -@@ -18107,10 +18107,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18184,10 +18184,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18257,10 +18257,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18317,10 +18317,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img(ind,cimg::mod(off,whds)); -+ if ((bool)img) return (double)img(ind,cimg::mod(off,whds)); - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18590,7 +18590,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -18662,7 +18662,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -19579,7 +19579,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -19648,7 +19648,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -25664,14 +25664,15 @@ - x0 = ((int)xc%width()) - width(), - y0 = ((int)yc%height()) - height(), - z0 = ((int)zc%depth()) - depth(), -- c0 = ((int)cc%spectrum()) - spectrum(); -+ c0 = ((int)cc%spectrum()) - spectrum(), -+ dx = width(), dy = height(), dz = depth(), dc = spectrum(); - #ifdef cimg_use_openmp - #pragma omp parallel for collapse(3) if (res.size()>=65536) - #endif -- for (int c = c0; c<(int)sc; c+=spectrum()) -- for (int z = z0; z<(int)sz; z+=depth()) -- for (int y = y0; y<(int)sy; y+=height()) -- for (int x = x0; x<(int)sx; x+=width()) -+ for (int c = c0; c<(int)sc; c+=dc) -+ for (int z = z0; z<(int)sz; z+=dz) -+ for (int y = y0; y<(int)sy; y+=dy) -+ for (int x = x0; x<(int)sx; x+=dx) - res.draw_image(x,y,z,c,*this); - } break; - case 1 : { // Neumann boundary. -@@ -47059,7 +47060,7 @@ - const IplImage *img = 0; - for (unsigned int i = 0; iwidthStep - 3*img->width); - assign(img->width,img->height,1,3); - const unsigned char* ptrs = (unsigned char*)img->imageData; -@@ -52636,7 +52637,7 @@ - case 'x' : { // Along the X-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx+=img._width; - dy = cimg::max(dy,img._height); - dz = cimg::max(dz,img._depth); -@@ -52646,7 +52647,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image(pos, -+ if ((bool)img) res.draw_image(pos, - (int)(align*(dy - img._height)), - (int)(align*(dz - img._depth)), - (int)(align*(dc - img._spectrum)), -@@ -52657,7 +52658,7 @@ - case 'y' : { // Along the Y-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy+=img._height; - dz = cimg::max(dz,img._depth); -@@ -52667,7 +52668,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - pos, - (int)(align*(dz - img._depth)), - (int)(align*(dc - img._spectrum)), -@@ -52678,7 +52679,7 @@ - case 'z' : { // Along the Z-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy = cimg::max(dy,img._height); - dz+=img._depth; -@@ -52688,7 +52689,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - (int)(align*(dy - img._height)), - pos, - (int)(align*(dc - img._spectrum)), -@@ -52699,7 +52700,7 @@ - default : { // Along the C-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy = cimg::max(dy,img._height); - dz = cimg::max(dz,img._depth); -@@ -52709,7 +52710,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - (int)(align*(dy - img._height)), - (int)(align*(dz - img._depth)), - pos, -@@ -53957,7 +53958,7 @@ - CImg img; - try { img.load_pnm(filename_tmp2); } - catch (CImgException&) { stop_flag = true; } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - } - cimg::exception_mode(omode); - if (is_empty()) -@@ -54033,7 +54034,7 @@ - CImg img; - try { img.load_png(filename_tmp2); } - catch (CImgException&) { } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - else { // Try to read animated gif. - unsigned int i = 0; - for (bool stop_flag = false; !stop_flag; ++i) { -@@ -54042,7 +54043,7 @@ - CImg img; - try { img.load_png(filename_tmp2); } - catch (CImgException&) { stop_flag = true; } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - } - } - cimg::exception_mode(omode); ---- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 -+++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 -@@ -1,4 +1,5 @@ - - PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 - PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) -- -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 ---- imager/MD5.orig 2016-09-12 15:08:55.000000000 +0200 -+++ imager/MD5 2017-04-01 22:44:16.943021224 +0200 -@@ -31,7 +31,7 @@ - 05e04a3bc5a858c40e001cc65b853dfc *inst/extdata/Leonardo_Birds.jpg - e1328ba2c55d5a72eb77e283c9630b90 *inst/extdata/parrots.png - daa5b7e30235689ad0444df37c88b7ff *inst/extdata/tennis_sif.mpeg --00de9e6b4c2066d28d7f8d9e251915cd *inst/include/CImg.h -+ea9acc61a3dd73452639c570af543d29 *inst/include/CImg.h - 034a9e8aab9e05094fd31ce9ea3bbae2 *inst/include/imager.h - 0c8aae8db902f96a8f8e323043eb1418 *inst/include/wrappers.h - be39be77874a0181ecd47b1a7a9af5dd *man/FFT.Rd -@@ -140,7 +140,7 @@ - a680472a2ef1eda48c1a9b90488543b5 *man/vanvliet.Rd - 08193940e20b440f614e4c7a2dbf82fb *man/warp.Rd - 429b25a38f282c30d5d178ad9efc3b1f *man/watershed.Rd --ab8f97aa6f15c67d1029e3eb5091853d *src/Makevars.in -+802ecbe76012c51adf729063804c793a *src/Makevars.in - 5ecf9e8577f31e535dee1c371e75a35f *src/Makevars.win - 78aff3a88c55983a329723eb1174a4ca *src/RcppExports.cpp - 8193f4fecd751c7d310d23b0faacd303 *src/colourspace.cpp diff --git a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch new file mode 100644 index 0000000000..8f3e05fe69 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -0,0 +1,310 @@ +fix compilation issues with Intel compilers in CImg.h +cfr. https://github.com/dtschump/CImg/issues/123 and https://github.com/dahtah/imager/commit/b46e96efe0a9c596c9aca9d786123b10dd83adf2 +also include extra compiler option -wd308 to avoid 'member "std::complex::_M_value" is inaccessible' errors +patched composed by Kenneth Hoste (HPC-UGent) +--- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 ++++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 +@@ -1,4 +1,5 @@ + + PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 + PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +diff --git a/inst/include/CImg.h b/inst/include/CImg.h +index 213d864..922edf8 100755 +--- a/inst/include/CImg.h ++++ b/inst/include/CImg.h +@@ -15161,7 +15161,7 @@ namespace cimg_library_suffixed { + const CImg& img_input=CImg::const_empty(), CImg *const img_output=0, + const CImgList *const list_input=0, CImgList *const list_output=0, + const bool _is_fill=false): +- code(_code),p_break((CImg*)0 - 2), ++ code(_code),p_break((CImg*)(-2*sizeof(CImg))), + imgin(img_input),listin(list_input?*list_input:CImgList::const_empty()), + imgout(img_output?*img_output:CImg::empty()),listout(list_output?*list_output:CImgList::empty()), + img_stats(_img_stats),list_stats(_list_stats),list_median(_list_median),user_macro(0), +@@ -15222,6 +15222,7 @@ namespace cimg_library_suffixed { + memtype.assign(mem._width,1,1,1,0); + for (unsigned int i = 0; i<_cimg_mp_slot_x; ++i) memtype[i] = 1; + memtype[17] = 0; ++ memtype[_cimg_mp_slot_x] = memtype[_cimg_mp_slot_y] = memtype[_cimg_mp_slot_z] = memtype[_cimg_mp_slot_c] = -2; + mempos = _cimg_mp_slot_c + 1; + variable_pos.assign(8); + +@@ -15270,7 +15271,7 @@ namespace cimg_library_suffixed { + } + + _cimg_math_parser(): +- code(_code),p_code_end(0),p_break((CImg*)0 - 2), ++ code(_code),p_code_end(0),p_break((CImg*)(-2*sizeof(CImg))), + imgin(CImg::const_empty()),listin(CImgList::const_empty()), + imgout(CImg::empty()),listout(CImgList::empty()), + img_stats(_img_stats),list_stats(_list_stats),list_median(_list_median),debug_indent(0), +@@ -15301,7 +15302,7 @@ namespace cimg_library_suffixed { + unsigned int *pd = res._data; + int level = 0; + for (const char *ps = expr._data; *ps && level>=0; ++ps) { +- if (!next_is_escaped && *ps=='\\') next_is_escaped = true; ++ if (!is_escaped && !next_is_escaped && *ps=='\\') next_is_escaped = true; + if (!is_escaped && *ps=='\'') { // Non-escaped character + if (!mode && ps>expr._data && *(ps - 1)=='[') next_mode = mode = 2; // Start vector-string + else if (mode==2 && *(ps + 1)==']') next_mode = !mode; // End vector-string +@@ -20498,7 +20499,7 @@ namespace cimg_library_suffixed { + CImg S(&_mp_arg(1) + 1,dx,dy,dz,dc,true); + const float opacity = (float)_mp_arg(12); + +- if (img) { ++ if (img._data) { + if (mp.opcode[13]!=~0U) { // Opacity mask specified + const ulongT sizM = mp.opcode[14]; + if (sizM<(ulongT)dx*dy*dz) +@@ -20605,7 +20606,7 @@ namespace cimg_library_suffixed { + off = (longT)_mp_arg(2), + whds = (longT)img.size(); + if (off>=0 && off=0 && off=0 && off=0 && off::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff=65536)) +- for (int c = c0; c<(int)sc; c+=spectrum()) +- for (int z = z0; z<(int)sz; z+=depth()) +- for (int y = y0; y<(int)sy; y+=height()) +- for (int x = x0; x<(int)sx; x+=width()) ++ for (int c = c0; c<(int)sc; c+=dc) ++ for (int z = z0; z<(int)sz; z+=dz) ++ for (int y = y0; y<(int)sy; y+=dy) ++ for (int x = x0; x<(int)sx; x+=dx) + res.draw_image(x,y,z,c,*this); + } break; + case 1 : { // Neumann +@@ -34824,8 +34826,7 @@ namespace cimg_library_suffixed { + _sigma_x = sigma_x>=0?sigma_x:-sigma_x*_width/100, + _sigma_y = sigma_y>=0?sigma_y:-sigma_y*_height/100, + _sigma_z = sigma_z>=0?sigma_z:-sigma_z*_depth/100, +- __sigma_r = sigma_r>=0?sigma_r:-sigma_r*(edge_max - edge_min)/100, +- _sigma_r = std::max(0.1f,__sigma_r), ++ _sigma_r = sigma_r>=0?sigma_r:-sigma_r*(edge_max - edge_min)/100, + _sampling_x = sampling_x?sampling_x:std::max(_sigma_x,1.0f), + _sampling_y = sampling_y?sampling_y:std::max(_sigma_y,1.0f), + _sampling_z = sampling_z?sampling_z:std::max(_sigma_z,1.0f), +@@ -48076,9 +48077,13 @@ namespace cimg_library_suffixed { + else return load_other(filename); + #else + // Open file and check for PNG validity +- const char *volatile nfilename = filename; // two 'volatile' here to remove a g++ warning due to 'setjmp'. ++#if defined __GNUC__ ++ const char *volatile nfilename = filename; // Use 'volatile' to avoid (wrong) g++ warning. + std::FILE *volatile nfile = file?file:cimg::fopen(nfilename,"rb"); +- ++#else ++ const char *nfilename = filename; ++ std::FILE *nfile = file?file:cimg::fopen(nfilename,"rb"); ++#endif + unsigned char pngCheck[8] = { 0 }; + cimg::fread(pngCheck,8,(std::FILE*)nfile); + if (png_sig_cmp(pngCheck,0,8)) { +@@ -49017,11 +49022,11 @@ namespace cimg_library_suffixed { + rdr.ndim(2)?rdr.ndim(2):1, + rdr.ndim(3)?rdr.ndim(3):1, + rdr.ndim(4)?rdr.ndim(4):1); +- if(typeid(T)==typeid(unsigned char)) ++ if (typeid(T)==typeid(unsigned char)) + rdr.setup_read_byte(); +- else if(typeid(T)==typeid(int)) ++ else if (typeid(T)==typeid(int)) + rdr.setup_read_int(); +- else if(typeid(T)==typeid(double)) ++ else if (typeid(T)==typeid(double)) + rdr.setup_read_double(); + else + rdr.setup_read_float(); +@@ -49312,7 +49317,7 @@ namespace cimg_library_suffixed { + *item = *tmp1 = *tmp2 = 0; + out[0] = std::fscanf(file,"%63s",item._data); + out[0] = out[1] = out[2] = out[3] = out[5] = 1; out[4] = out[6] = out[7] = -1; +- if(cimg::strncasecmp(item,"#INRIMAGE-4#{",13)!=0) ++ if (cimg::strncasecmp(item,"#INRIMAGE-4#{",13)!=0) + throw CImgIOException("CImg<%s>::load_inr(): INRIMAGE-4 header not found.", + pixel_type()); + +@@ -49342,17 +49347,17 @@ namespace cimg_library_suffixed { + tmp2._data); + } + } +- if(out[0]<0 || out[1]<0 || out[2]<0 || out[3]<0) ++ if (out[0]<0 || out[1]<0 || out[2]<0 || out[3]<0) + throw CImgIOException("CImg<%s>::load_inr(): Invalid dimensions (%d,%d,%d,%d) defined in header.", + pixel_type(), + out[0],out[1],out[2],out[3]); +- if(out[4]<0 || out[5]<0) ++ if (out[4]<0 || out[5]<0) + throw CImgIOException("CImg<%s>::load_inr(): Incomplete pixel type defined in header.", + pixel_type()); +- if(out[6]<0) ++ if (out[6]<0) + throw CImgIOException("CImg<%s>::load_inr(): Incomplete PIXSIZE field defined in header.", + pixel_type()); +- if(out[7]<0) ++ if (out[7]<0) + throw CImgIOException("CImg<%s>::load_inr(): Big/Little Endian coding type undefined in header.", + pixel_type()); + } +@@ -52161,9 +52166,16 @@ namespace cimg_library_suffixed { + "save_png(): Unable to save data in '(*FILE)' unless libpng is enabled.", + cimg_instance); + #else +- const char *volatile nfilename = filename; // two 'volatile' here to remove a g++ warning due to 'setjmp'. ++ ++#if defined __GNUC__ ++ const char *volatile nfilename = filename; // Use 'volatile' to avoid (wrong) g++ warning. + std::FILE *volatile nfile = file?file:cimg::fopen(nfilename,"wb"); + volatile double stmin, stmax = (double)max_min(stmin); ++#else ++ const char *nfilename = filename; ++ std::FILE *nfile = file?file:cimg::fopen(nfilename,"wb"); ++ double stmin, stmax = (double)max_min(stmin); ++#endif + + if (_depth>1) + cimg::warn(_cimg_instance +@@ -52188,7 +52200,7 @@ namespace cimg_library_suffixed { + png_error_ptr user_error_fn = 0, user_warning_fn = 0; + png_structp png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING,user_error_ptr, user_error_fn, + user_warning_fn); +- if(!png_ptr){ ++ if (!png_ptr){ + if (!file) cimg::fclose(nfile); + throw CImgIOException(_cimg_instance + "save_png(): Failed to initialize 'png_ptr' structure when saving file '%s'.", +@@ -52921,17 +52933,17 @@ namespace cimg_library_suffixed { + wtr.open(filename, imitate_file); + else { + minc::minc_info di; +- if(width()) di.push_back(minc::dim_info(width(),width()*0.5,-1,minc::dim_info::DIM_X)); +- if(height()) di.push_back(minc::dim_info(height(),height()*0.5,-1,minc::dim_info::DIM_Y)); +- if(depth()) di.push_back(minc::dim_info(depth(),depth()*0.5,-1,minc::dim_info::DIM_Z)); +- if(spectrum()) di.push_back(minc::dim_info(spectrum(),spectrum()*0.5,-1,minc::dim_info::DIM_TIME)); ++ if (width()) di.push_back(minc::dim_info(width(),width()*0.5,-1,minc::dim_info::DIM_X)); ++ if (height()) di.push_back(minc::dim_info(height(),height()*0.5,-1,minc::dim_info::DIM_Y)); ++ if (depth()) di.push_back(minc::dim_info(depth(),depth()*0.5,-1,minc::dim_info::DIM_Z)); ++ if (spectrum()) di.push_back(minc::dim_info(spectrum(),spectrum()*0.5,-1,minc::dim_info::DIM_TIME)); + wtr.open(filename,di,1,NC_FLOAT,0); + } +- if(typeid(T)==typeid(unsigned char)) ++ if (typeid(T)==typeid(unsigned char)) + wtr.setup_write_byte(); +- else if(typeid(T)==typeid(int)) ++ else if (typeid(T)==typeid(int)) + wtr.setup_write_int(); +- else if(typeid(T)==typeid(double)) ++ else if (typeid(T)==typeid(double)) + wtr.setup_write_double(); + else + wtr.setup_write_float(); +@@ -56443,7 +56455,7 @@ namespace cimg_library_suffixed { + } + if (disp.is_resized()) { disp.resize(false); visu0.assign(); } + if (ym>=0 && ym<13) { if (!text_down) { visu.assign(); text_down = true; }} +- else if (ym>=visu.height() - 13) { if(text_down) { visu.assign(); text_down = false; }} ++ else if (ym>=visu.height() - 13) { if (text_down) { visu.assign(); text_down = false; }} + if (!exit_on_anykey && key && key!=cimg::keyESC && + (key!=cimg::keyW || (!disp.is_keyCTRLLEFT() && !disp.is_keyCTRLRIGHT()))) { + key = 0; +@@ -57564,7 +57576,7 @@ namespace cimg_library_suffixed { + if (nlast_frame>=nb_images) nlast_frame = nb_images - 1; + assign(1 + (nlast_frame - nfirst_frame)/nstep_frame); + TIFFSetDirectory(tif,0); +-#if cimg_verbosity>=3 ++#if cimg_verbosity<3 + TIFFSetWarningHandler(0); + TIFFSetErrorHandler(0); + #endif +@@ -58324,7 +58336,6 @@ namespace cimg_library_suffixed { + throw CImgIOException(_cimglist_instance + "save_gzip_external(): Specified filename is (null).", + cimglist_instance); +- + CImg command(1024), filename_tmp(256), body(256); + const char + *ext = cimg::split_filename(filename,body), +--- imager/src/Makevars.in.orig 2017-04-04 18:02:36.525410690 +0200 ++++ imager/src/Makevars.in 2017-04-04 18:04:52.818449342 +0200 +@@ -1,3 +1,5 @@ + PKG_CPPFLAGS = $(SHLIB_OPENMP_CFLAGS) @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ @TIFF_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' + PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ @TIFF_LIBS@ $(RCPP_LDFLAGS) + ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 7638aeafcfa7264556a6ad330ed7572759665261 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:08:33 +0200 Subject: [PATCH 681/818] added zlib dependency --- .../easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb index c3aab419f3..773f70da96 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.18')] +dependencies = [ + ('libpng', '1.6.18'), + ('zlib', '1.2.8') +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From e814354fd0809d35cbf6bf1b85844bb2e267dcfc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:09:15 +0200 Subject: [PATCH 682/818] added zlib dependency --- .../easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb index 76cd412cf3..7436cc5833 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('zlib', '1.2.8') +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From d90ac78aec452f629244a06ae4ff49c8001e7684 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:10:43 +0200 Subject: [PATCH 683/818] added custom sanity check --- .../easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb index a083925f91..2a604f301f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -16,4 +16,11 @@ dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' -- GitLab From ab8b2b9c6a5272d9912cff51be3bb22a5eff1b3e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:11:13 +0200 Subject: [PATCH 684/818] added custom sanity checks --- .../easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb index cb4fbebab2..15f766ff31 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -16,4 +16,11 @@ dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' -- GitLab From 746c112e1e9293ed92e4ea7192c1f6271ad17621 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:12:12 +0200 Subject: [PATCH 685/818] remove unneeded line --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 14c2e7f378..9cef816ccd 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -24,7 +24,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('six', '1.10.0', { -- GitLab From a00d479e8b57814916e4d9078bda040ef48fe56f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:15:01 +0200 Subject: [PATCH 686/818] delete unneeded LD_LIBRARY_PATH --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 9cef816ccd..9565d51bb3 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -66,7 +66,6 @@ exts_list = [ modextrapaths = { 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], - 'LD_LIBRARY_PATH': ['lib/python%(pyshortver)s/site-packages'] } sanity_check_paths = { -- GitLab From 4b6fe00282e6767b906ebac0a88c360b0c42300d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:15:22 +0200 Subject: [PATCH 687/818] update sanity check --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 9565d51bb3..52da5ecd72 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -70,7 +70,7 @@ modextrapaths = { sanity_check_paths = { 'files': ['bin/multiqc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/multiqc-%(version)s-py%(pyshortver)s.egg'] + 'dirs': ['lib/python%(pyshortver)s/site-packages/'] } moduleclass = 'bio' -- GitLab From cc5d41bc0cc73c26f134801cede7f89961d06811 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:29:23 +0930 Subject: [PATCH 688/818] Easyconfig for Autotools-20150215/foss-2015b --- .../Autotools/Autotools-20150215-foss-2015b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb new file mode 100644 index 0000000000..ab4ec5f149 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' -- GitLab From c65c50b2a84609923b11eebb2dfe79b7c1252752 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:30:11 +0930 Subject: [PATCH 689/818] Added comment/author to patch file --- .../easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch index a88701ea28..735a5b6d0c 100644 --- a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -1,3 +1,6 @@ +The Open Sourcing and refactoring of BioKanga on GitHub has resulted in some build issues. This +patch removes references to code which nolonger exists in refactored code of v4.3.4 +author: Nathan S. Watson-Haigh (University of Adelaide) --- ./configure.ac 2017-04-04 11:47:18.067209892 +0930 +++ ./configure.ac 2017-04-04 11:47:46.719519662 +0930 @@ -23,11 +23,10 @@ -- GitLab From 62b4678f29b9ba66d2d7334bf916a5871aa08573 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:31:32 +0930 Subject: [PATCH 690/818] Implement changes suggested by Kenneth Hoste. * Changed to use Autotools-20150215/foss-2015b as build dependency. * Use %(version)s variable in patch name instead of hardcoding. --- .../easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb index da082e4501..b413e97fee 100644 --- a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -13,12 +13,9 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['BioKanga-4.3.4_configure.patch'] +patches = ['BioKanga-%(version)s_configure.patch'] -builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15') -] +builddependencies = [('Autotools', '20150215')] preconfigopts = "autoreconf -f -i && " -- GitLab From fa83d2fc94fcabf75adbd75cde9c2ce86d225162 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:49:56 +0930 Subject: [PATCH 691/818] Adding libtool-2.4.6/foss-2015b missing dep --- .../l/libtool/libtool-2.4.6-foss-2015b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb new file mode 100644 index 0000000000..83d12ef5f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' -- GitLab From 71e29e140a369ff5d938a57835bda6f4f53e5d1f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 5 Apr 2017 09:00:59 +0200 Subject: [PATCH 692/818] removed unused patches line --- .../n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb index b4a5ec30e9..a4c16330cb 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -14,8 +14,6 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -#patches = ['numpy-1.8.0-mkl.patch'] - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From cad67753370e1950e1ee1c63301ea5b159276d0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 11:23:41 +0200 Subject: [PATCH 693/818] bump imager extension to 0.40.1 in R 3.3.3 easyconfig to sync it up with #4427 --- easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 2584758870..3b6ee9a746 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -502,7 +502,8 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', ext_options), ] moduleclass = 'lang' -- GitLab From fc93911bf77c7d56dcb1b7fbf7c1e01b91116208 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 5 Apr 2017 13:03:36 +0200 Subject: [PATCH 694/818] style fixes and add symlink to the sanity check --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb index cd17c8d34d..c6c18b59b8 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -18,8 +18,10 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + sanity_check_paths = { - 'files': ['sambamba_v%(version)s'], + 'files': ['sambamba_v%(version)s', 'sambamba'], 'dirs': [], } @@ -27,6 +29,4 @@ modextrapaths = { 'PATH': "", } -postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] - moduleclass = 'bio' -- GitLab From ff2de14ad7c936a63b9c2b9ba092ff0912669456 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 Apr 2017 12:03:45 +0100 Subject: [PATCH 695/818] Add explicit Python extension deps, based on @pescobar's work --- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 54 +++++++++++++++++-- 1 file changed, 50 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb index a7a94c8c8c..4ca3af6861 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -1,7 +1,11 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Adam Huffman # The Francis Crick Institute -easyblock = 'PythonPackage' +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' name = 'MultiQC' version = '0.9' @@ -16,14 +20,56 @@ description = """Aggregate results from bioinformatics analyses across many samp toolchain = {'name': 'foss', 'version': '2016b'} -sources = ['v%(version)s.tar.gz'] -source_urls = ['https://github.com/ewels/MultiQC/archive'] - dependencies = [ ('Python', '2.7.12'), ('matplotlib', '2.0.0', versionsuffix), ] +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('pyparsing', '2.1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('pytz', '2016.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + }), + ('python-dateutil', '2.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('PyYAML', '3.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('multiqc', version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['lib/python%(pyshortver)s/site-packages'] -- GitLab From fa8ca0b1d95b064584aaf1b3885d72ebfc7a3366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 14:26:20 +0200 Subject: [PATCH 696/818] adding easyconfigs: vsc-mympirun-4.0.0b0.eb, vsc-base-2.5.8.eb, IPy-0.83.eb, vsc-install-0.10.25.eb --- easybuild/easyconfigs/i/IPy/IPy-0.83.eb | 23 ++++++++++++ .../easyconfigs/v/vsc-base/vsc-base-2.5.8.eb | 27 ++++++++++++++ .../v/vsc-install/vsc-install-0.10.25.eb | 23 ++++++++++++ .../v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 35 +++++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPy/IPy-0.83.eb create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb create mode 100644 easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb diff --git a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb new file mode 100644 index 0000000000..661784d022 --- /dev/null +++ b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'IPy' +version = '0.83' + +homepage = 'https://pypi.python.org/pypi/IPy' +description = """Class and tools for handling of IPv4 and IPv6 addresses and networks""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'IPy'} + +shortpyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/' % shortpyver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb new file mode 100644 index 0000000000..c38a164cb9 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'vsc-base' +version = '2.5.8' + +homepage = 'http://hpcugent.github.com/vsc-base/' +description = """Basic Python libraries used by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +# install as zipped egg to make sure that tools that use this as a dependency are responsive +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'vsc.utils'} + +shortpyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%(pyver)s/site-packages/vsc_base-%%(version)s-py%(pyver)s.egg' % {'pyver': shortpyver}], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb new file mode 100644 index 0000000000..c821c18048 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.10.25' + +homepage = 'http://hpcugent.github.com/vsc-install/' +description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.install'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb new file mode 100755 index 0000000000..58a69d638c --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '4.0.0b0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = ['vsc-mympirun-%(version)s.tar.gz'] + +dependencies = [ + ('vsc-base', '2.5.8'), + ('IPy', '0.83'), +] +builddependencies = [('vsc-install', '0.10.25')] + +#postinstallcmds = ['echo "import pkg_resources; pkg_resources.declare_namespace(__name__)" > %(installdir)s/lib/vsc/__init__.py'] +#use_easy_install = True + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +#options = {'modulename': 'vsc.mympirun'} +options = {'modulename': 'vsc'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 03f367f888b40140a128276d63c9ff7c7f4779bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 14:30:31 +0200 Subject: [PATCH 697/818] don't patch Makevars.in twice in patch for R imager extension --- .../easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch index 8f3e05fe69..829b112342 100644 --- a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -2,15 +2,6 @@ fix compilation issues with Intel compilers in CImg.h cfr. https://github.com/dtschump/CImg/issues/123 and https://github.com/dahtah/imager/commit/b46e96efe0a9c596c9aca9d786123b10dd83adf2 also include extra compiler option -wd308 to avoid 'member "std::complex::_M_value" is inaccessible' errors patched composed by Kenneth Hoste (HPC-UGent) ---- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 -+++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 -@@ -1,4 +1,5 @@ - - PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 - PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) -- -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 diff --git a/inst/include/CImg.h b/inst/include/CImg.h index 213d864..922edf8 100755 --- a/inst/include/CImg.h -- GitLab From 6806348b71dbd35af608f2da2a6644e741ae03d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:00:10 +0200 Subject: [PATCH 698/818] remove commented out lines, addd sanity check command to check that 'mympirun --help' works --- .../easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb index 58a69d638c..b31dee5a6e 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -17,13 +17,10 @@ dependencies = [ ] builddependencies = [('vsc-install', '0.10.25')] -#postinstallcmds = ['echo "import pkg_resources; pkg_resources.declare_namespace(__name__)" > %(installdir)s/lib/vsc/__init__.py'] -#use_easy_install = True - # we ship something in bin/fake modextrapaths = {'PATH': 'bin/fake'} -#options = {'modulename': 'vsc.mympirun'} +# can't check for 'import vsc.mympirun' because vsc-base may be installed system-wide options = {'modulename': 'vsc'} pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) @@ -32,4 +29,6 @@ sanity_check_paths = { 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], } +sanity_check_commands = ["mympirun --help"] + moduleclass = 'tools' -- GitLab From 372ee603a6f226341a0ee51b8a6b33cdb48156e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:14:17 +0200 Subject: [PATCH 699/818] bump to intel/2017a and Perl 5.24.1 in ROI_PAC easyconfig --- ....2-intel-2016b.eb => GETORB-2.3.2-intel-2017a.eb} | 2 +- ...0.eb => ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb} | 12 ++++++++---- 2 files changed, 9 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/g/GETORB/{GETORB-2.3.2-intel-2016b.eb => GETORB-2.3.2-intel-2017a.eb} (92%) rename easybuild/easyconfigs/r/ROI_PAC/{ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb => ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb} (83%) diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb similarity index 92% rename from easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb rename to easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb index 2e648643f9..f01c7d1564 100644 --- a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb @@ -6,7 +6,7 @@ version = '2.3.2' homepage = 'http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml' description = "GETORB software package contains programs to handle the orbital data records (ODRs)" -toolchain = {'name': 'intel', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] sources = ['getorb_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb similarity index 83% rename from easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb rename to easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb index 89a80fb749..351c02bb8c 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -8,22 +8,26 @@ homepage = 'http://roipac.org/' description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data to produce differential interferograms""" -toolchain = {'name': 'intel', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} # download of ROI_PAC tarball requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] # make_raw_alos.pl via http://roipac.org/cgi-bin/moin.cgi/ALOS_PALSAR?action=AttachFile&do=get&target=make_raw_alos.pl patches = [ - 'ROI_PAC-%(version)s_fix-IntSim.patch', ('make_raw_alos.pl', 'ROI_PAC/INT_SCR'), + 'ROI_PAC-%(version)s_fix-IntSim.patch', +] +checksums = [ + 'db50e9cd99183291eb9cfe7c74750cc6', # ROI_PAC_3_0_1.tgz + '284faa43c12626670810c1e14d393159', # make_raw_alos.pl ] builddependencies = [('Autotools', '20150215')] dependencies = [ ('FFTW', '3.3.6'), ('GETORB', '2.3.2'), - ('Perl', '5.24.0'), + ('Perl', '5.24.1'), ] start_dir = 'ROI_PAC' @@ -52,6 +56,6 @@ modextravars = { 'ROI_PAC': '%(installdir)s', } -modloadmsg = "To define: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" +modloadmsg = "These environment variables should be defined: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" moduleclass = 'geo' -- GitLab From 3db3b7b5770a9f83fd0aa56f48c62b8eb4410f80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:15:16 +0200 Subject: [PATCH 700/818] add missing patch file for ROI_PAC --- .../r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch new file mode 100644 index 0000000000..f9b938a005 --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch @@ -0,0 +1,15 @@ +fix bug in ROI_PAC v3.0.1, cfr. http://roipac.org/cgi-bin/moin.cgi/Patches +--- ./ROI_PAC/intsim/IntSim.f.orig 2017-03-30 10:35:09.702908447 +0200 ++++ ./ROI_PAC/intsim/IntSim.f 2017-03-30 10:36:32.204116436 +0200 +@@ -1339,6 +1339,11 @@ + ntotlonpx = ntotcpx + endif + ++! update these after padding has been applied EJF 2013/5/9 ++ nslatpx = int(dem_pixel_min(1)) ++ nslonpx = int(dem_pixel_min(2)) ++ nlatpx = nint(dem_pixel_max(1)) - nslatpx + 1 ++ nlonpx = nint(dem_pixel_max(2)) - nslonpx + 1 + + write (*,*) + write (*,*) -- GitLab From 231a282bc419ebf00eb44efadcd54d9ca68bfca1 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 4 Apr 2017 18:48:52 +0000 Subject: [PATCH 701/818] Fix pkgconfig patch for Qhull to only let CMake substitute @ --- easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 53f43a015d..0aa79c3083 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -3,7 +3,7 @@ requires making CMake to fill in the gaps via 'configure_file(... @ONLY)' author: Kenneth Hoste (UGent) --- qhull/CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 +++ qhull/CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 -@@ -430,3 +430,9 @@ +@@ -430,3 +430,10 @@ install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) @@ -11,6 +11,7 @@ author: Kenneth Hoste (UGent) +CONFIGURE_FILE( + "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" + "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" ++ @ONLY +) +INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) --- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 -- GitLab From f5d42fd9a077f9483e3e48fae1daee3bd335347e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 00:10:18 +0200 Subject: [PATCH 702/818] fix comment --- .../r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb index 351c02bb8c..d772d057cf 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -37,7 +37,7 @@ installopts = "&& cd fip && $CC $CFLAGS -o add_rmgAmpPhs add_rmgAmpPhs.c && cp - postinstallcmds = [ # symlink to getorb requires in /bin subdirectory "cd %(installdir)s/bin && ln -s $(which getorb)", - # also copy scripts and make sure they're excutable + # also copy scripts "cp -a INT_SCR/* %(installdir)s/bin", # fix shebang in Perl scripts "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//bin/*.pl", -- GitLab From d8cc0f780474286401a29f65cc0fe227c987b28a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 00:51:01 +0000 Subject: [PATCH 703/818] Octave 4.2.1: add easyconfig for intel 2016b with updated deps incl Qt5 --- .../o/Octave/Octave-4.2.1-intel-2016b.eb | 63 +++++++++++++++++++ .../o/Octave/Octave-4.2.1_intel.patch | 47 ++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb new file mode 100644 index 0000000000..5ea3487cef --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.2.1' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.3'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20170314'), + ('PCRE', '8.40'), + ('ncurses', '6.0'), + ('libreadline', '7.0'), + ('arpack-ng', '3.4.0'), + ('cURL', '7.52.1'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.12.1'), + ('freetype', '2.7'), + ('GLPK', '4.60'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.5'), + ('Java', '1.8.0_121', '', True), + ('zlib', '1.2.8'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt5', '5.8.0'), + ('HDF5', '1.8.17', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.6'), +] + +configopts = 'MOC=$EBROOTQT5/bin/moc ' +configopts += 'UIC=$EBROOTQT5/bin/uic ' +configopts += 'RCC=$EBROOTQT5/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch new file mode 100644 index 0000000000..872aa06961 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch @@ -0,0 +1,47 @@ +Intel compiler does not understand __builtin_*_overflow +# Oct 25th 2016 by B. Hajgato (Free University Brussels - VUB) +# Apr 4th 2017 by B. Oldeman (Compute Canada) +--- octave-4.2.1/libgnu/xalloc-oversized.h.orig 2017-02-22 18:17:37.000000000 +0000 ++++ octave-4.2.1/libgnu/xalloc-oversized.h 2017-04-04 14:29:22.020046084 +0000 +@@ -43,12 +43,12 @@ + nonnegative. This is a macro, not a function, so that it + works correctly even when SIZE_MAX < N. */ + +-#if 7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p) ++#if (7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p) && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) __builtin_mul_overflow_p (n, s, (size_t) 1) + #elif ((5 <= __GNUC__ \ + || (__has_builtin (__builtin_mul_overflow) \ + && __has_builtin (__builtin_constant_p))) \ +- && !__STRICT_ANSI__) ++ && !__STRICT_ANSI__ && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) \ + (__builtin_constant_p (n) && __builtin_constant_p (s) \ + ? __xalloc_oversized (n, s) \ +--- octave-4.0.3/libgnu/glob.c.orig 2016-10-24 16:11:56.437441986 +0200 ++++ octave-4.0.3/libgnu/glob.c 2016-10-24 16:12:21.127612656 +0200 +@@ -257,7 +257,7 @@ + static bool + size_add_wrapv (size_t a, size_t b, size_t *r) + { +-#if 5 <= __GNUC__ || __has_builtin (__builtin_add_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + return __builtin_add_overflow (a, b, r); + #else + *r = a + b; +--- octave-4.2.1/libgnu/intprops.h.orig 2017-02-22 18:17:35.000000000 +0000 ++++ octave-4.2.1/libgnu/intprops.h 2017-04-04 14:35:17.208604138 +0000 +@@ -242,11 +242,11 @@ + + /* True if __builtin_add_overflow (A, B, P) works when P is non-null. */ + #define _GL_HAS_BUILTIN_OVERFLOW \ +- (5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) ++ ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + + /* True if __builtin_add_overflow_p (A, B, C) works. */ + #define _GL_HAS_BUILTIN_OVERFLOW_P \ +- (7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p)) ++ ((7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p)) && !__INTEL_COMPILER) + + /* The _GL*_OVERFLOW macros have the same restrictions as the + *_RANGE_OVERFLOW macros, except that they do not assume that operands -- GitLab From 8fde62045a9e2e96adb7ce875c72d3b922ee411a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 01:06:14 +0000 Subject: [PATCH 704/818] Fix irresolvable dependencies. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 5ea3487cef..7cb6f50189 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -22,10 +22,10 @@ builddependencies = [ ] dependencies = [ - ('X11', '20170314'), + ('X11', '20160819'), ('PCRE', '8.40'), ('ncurses', '6.0'), - ('libreadline', '7.0'), + ('libreadline', '6.3'), ('arpack-ng', '3.4.0'), ('cURL', '7.52.1'), ('FLTK', '1.3.3'), -- GitLab From 950cd4fa74caec7d7129c9c5f17923778748f88e Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 01:24:41 +0000 Subject: [PATCH 705/818] Avoid conflicts in dependencies. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 7cb6f50189..e845e9c89e 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['%(name)s-%(version)s_intel.patch'] builddependencies = [ ('Bison', '3.0.4'), - ('flex', '2.6.3'), + ('flex', '2.6.2'), ('Autotools', '20150215'), ('libtool', '2.4.6'), ('gperf', '3.0.4'), @@ -23,14 +23,14 @@ builddependencies = [ dependencies = [ ('X11', '20160819'), - ('PCRE', '8.40'), + ('PCRE', '8.39'), ('ncurses', '6.0'), ('libreadline', '6.3'), ('arpack-ng', '3.4.0'), ('cURL', '7.52.1'), ('FLTK', '1.3.3'), ('fontconfig', '2.12.1'), - ('freetype', '2.7'), + ('freetype', '2.6.5'), ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), -- GitLab From 16d28a2efc5c9070ab7bc996dd5221a5e676e15b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Apr 2017 07:59:23 +0200 Subject: [PATCH 706/818] adding easyconfigs: Autotools-20150215-GCCcore-5.4.0.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb | 29 +++++++++++++++ .../a/Automake/Automake-1.15-GCCcore-5.4.0.eb | 36 +++++++++++++++++++ .../Autotools-20150215-GCCcore-5.4.0.eb | 18 ++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 20 +++++++++++ 4 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..765fe6f2fd --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..0d4c530534 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..79f6723eb6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] +# Pure bundle -- no need to specify 'binutils' used when building GCCcore toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..677b163091 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'lib' -- GitLab From 5e3ae80f025fa5ee94d3d58603d6b2f037b68c10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 08:52:34 +0200 Subject: [PATCH 707/818] adding easyconfigs: StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb, snaphu-1.4.2-intel-2017a.eb, Triangle-1.6-intel-2017a.eb --- .../StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb | 50 +++++++++++++++++++ .../s/snaphu/snaphu-1.4.2-intel-2017a.eb | 26 ++++++++++ .../t/Triangle/Triangle-1.6-intel-2017a.eb | 34 +++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb create mode 100644 easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..457a515e11 --- /dev/null +++ b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'StaMPS' +version = '3.3b1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://homepages.see.leeds.ac.uk/~earahoo/stamps/' +description = """A software package to extract ground displacements from time series of synthetic aperture radar + (SAR) acquisitions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://homepages.see.leeds.ac.uk/~earahoo/stamps/'] +sources = ['%(name)s_v%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.1'), + ('ROI_PAC', '3.0.1', versionsuffix), + ('Doris', '4.02'), + ('Triangle', '1.6'), + ('snaphu', '1.4.2'), +] + +skipsteps = ['configure'] + +start_dir = 'src' + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS"' + +preinstallopts = 'cp -a ../bin %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin && cd .. && cp -a {DORIS_SCR,matlab,ROI_PAC_SCR} %(installdir)s/' + +postinstallcmds = [ + # fix shebang in Perl scripts + "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//*_SCR/*.pl", +] + +sanity_check_paths = { + 'files': ['bin/calamp', 'bin/cpxsum', 'bin/pscdem', 'bin/psclonlat', 'bin/pscphase', 'bin/selpsc_patch', + 'bin/selsbc_patch', 'bin/selsbc_patch_new'], + 'dirs': ['DORIS_SCR', 'matlab', 'ROI_PAC_SCR'], +} + +modextravars = { + 'DORIS_SCR': '%(installdir)s/DORIS_SCR', + 'MY_SCR': '%(installdir)s/ROI_PAC_SCR', + 'STAMPS': '%(installdir)s', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb new file mode 100644 index 0000000000..467c802a40 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb new file mode 100644 index 0000000000..166329f4f1 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 974ebcbcc6544aac2c3e1b84ca1fe3529d85bbe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 09:54:44 +0200 Subject: [PATCH 708/818] {bio}[intel/2017a] BreakDancer 1.4.5 --- .../BreakDancer-1.4.5-intel-2017a.eb | 29 +++++++++++++++++++ ...eakDancer-1.4.5_fix-icpc-compilation.patch | 14 +++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb new file mode 100644 index 0000000000..2526494ae8 --- /dev/null +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'BreakDancer' +version = '1.4.5' + +homepage = 'http://gmt.genome.wustl.edu/packages/breakdancer' +description = """BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from + next generation paired-end sequencing reads""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/genome/breakdancer/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['BreakDancer-%(version)s_fix-icpc-compilation.patch'] + +dependencies = [('zlib', '1.2.11')] +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=release' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/breakdancer-max'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch new file mode 100644 index 0000000000..e2859dd505 --- /dev/null +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch @@ -0,0 +1,14 @@ +fix for compilation error: +error: no instance of constructor "testing::AssertionResult::AssertionResult" matches the argument list +author: Kenneth Hoste (HPC-UGent) +--- test/lib/io/TestBam.cpp.orig 2017-04-03 18:06:43.355151223 +0200 ++++ test/lib/io/TestBam.cpp 2017-04-03 18:06:09.154756888 +0200 +@@ -107,7 +107,7 @@ + size_t size = in.tellg(); + in.seekg(0, std::ios::beg); + std::vector buf(size); +- ASSERT_TRUE(in.read(buf.data(), size)); ++ ASSERT_TRUE((bool)in.read(buf.data(), size)); + buf.push_back(0); // make sure buffer is null terminated + EXPECT_STREQ(samData.c_str(), buf.data()); + -- GitLab From f092fd499ca51fff05161c17c43d49e84315d7e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 10:07:38 +0200 Subject: [PATCH 709/818] also include $LDFLAGS --- .../s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb | 2 +- easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb index 457a515e11..122fdfc60d 100644 --- a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb @@ -25,7 +25,7 @@ skipsteps = ['configure'] start_dir = 'src' -buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS"' +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS $LDFLAGS"' preinstallopts = 'cp -a ../bin %(installdir)s/bin && ' installopts = 'INSTALL_DIR=%(installdir)s/bin && cd .. && cp -a {DORIS_SCR,matlab,ROI_PAC_SCR} %(installdir)s/' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb index 8397d4ea59..c65762eb7a 100644 --- a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb @@ -14,7 +14,7 @@ sources = ['snaphu-v%(version)s.tar.gz'] start_dir = 'src' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' files_to_copy = ['bin', 'config', 'man'] diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb index 467c802a40..3261c207aa 100644 --- a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -14,7 +14,7 @@ sources = ['snaphu-v%(version)s.tar.gz'] start_dir = 'src' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' files_to_copy = ['bin', 'config', 'man'] -- GitLab From 94e004a50d650754e599fc04bf206b24cfeb96ab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Apr 2017 11:33:25 +0200 Subject: [PATCH 710/818] adding easyconfigs: freetype-2.7.1-GCCcore-5.4.0.eb --- .../b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb | 18 ++++++++++++ .../freetype/freetype-2.7.1-GCCcore-5.4.0.eb | 29 +++++++++++++++++++ .../l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb | 29 +++++++++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 25 ++++++++++++++++ 4 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..139b8c3f30 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..fee6777ad0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.28'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..3d37620c50 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.28' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..8409e2aa5c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 9b6f95e5909ef012e1853fba226f146c6b9428c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 12:32:58 +0200 Subject: [PATCH 711/818] adding easyconfigs: BLAT-3.5-intel-2017a.eb --- .../b/BLAT/BLAT-3.5-intel-2017a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb new file mode 100644 index 0000000000..7e57ded042 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity + of length 25 bases or more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://users.soe.ucsc.edu/~kent/src'] + +dependencies = [('libpng', '1.6.29')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 927716f4af5f0146eb885b5debdd96c471bae27e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 12:33:26 +0200 Subject: [PATCH 712/818] adding easyconfigs: BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb --- .../BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..43055f9bb9 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,28 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.24.1'), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From be8d72e960b3f118bb72ba5070687d21bbf28928 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 13:25:25 +0200 Subject: [PATCH 713/818] adding easyconfigs: Rascaf-1.0.2-intel-2017a.eb, SAMtools-0.1.20-intel-2017a.eb --- .../r/Rascaf/Rascaf-1.0.2-intel-2017a.eb | 33 +++++++++++++++++++ .../s/SAMtools/SAMtools-0.1.20-intel-2017a.eb | 20 +++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb diff --git a/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb new file mode 100644 index 0000000000..8d81791c83 --- /dev/null +++ b/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'Rascaf' +version = '1.0.2' + +homepage = 'https://github.com/mourisl/Rascaf' +description = """Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads + to improve a draft assembly, particularly in the gene regions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/mourisl/Rascaf/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '0.1.20'), +] + +# create fake libbam.a to skip building of included SAMtools +prebuildopts = "touch samtools-0.1.19/libbam.a && " +# empty LINKPATH to avoid that included SAMtools copy is used +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" LINKPATH=""' +parallel = 1 + +files_to_copy = [(['rascaf', 'rascaf-join'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rascaf', 'bin/rascaf-join'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb new file mode 100644 index 0000000000..75a920a136 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb @@ -0,0 +1,20 @@ +name = 'SAMtools' +version = '0.1.20' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/samtools/%(namelower)s/archive/%(version)s'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' -- GitLab From 5977c9c92fa12f6fefb43d24dc7ed36a80da51bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 13:41:48 +0200 Subject: [PATCH 714/818] adding easyconfigs: Boost-1.63.0-intel-2017a-Python-2.7.13.eb --- .../Boost-1.63.0-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e0340fc524 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 11b3a84303b558a60d035b91a785884b116774f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:11:47 +0200 Subject: [PATCH 715/818] adding easyconfigs: SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb --- ...ACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..9d51ecf299 --- /dev/null +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'SSPACE_Basic' +version = '2.1.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/nsoranzo/sspace_basic' +description = "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/nsoranzo/sspace_basic/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.1'), + ('Bowtie', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['README', 'SSPACE_Basic.pl'], + 'dirs': ['bin', 'tools'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From b921145d0ec6fb2ef6480dbef2b506f4faf241c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:47:04 +0200 Subject: [PATCH 716/818] {bio}[intel/2017a] GapFiller v2.1.1 --- .../GapFiller/GapFiller-2.1.1-intel-2017a.eb | 30 +++++++++++++++++++ .../GapFiller/GapFillter-2.1.1_fix-typo.patch | 13 ++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb new file mode 100644 index 0000000000..4e408b39dd --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GapFiller' +version = '2.1.1' + +homepage = 'https://sourceforge.net/projects/gapfiller' +description = """GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. + It can be used for both DNA and RNA and it has been tested on Illumina data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['GapFillter-%(version)s_fix-typo.patch'] + +dependencies = [ + ('Boost', '1.63.0', '-Python-2.7.13'), + ('zlib', '1.2.11'), +] + +buildopts = 'bin_PROGRAMS=GapFiller ' +buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"' +installopts = 'bin_PROGRAMS=GapFiller ' + +sanity_check_paths = { + 'files': ['bin/GapFiller'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch b/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch new file mode 100644 index 0000000000..4327a994ef --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch @@ -0,0 +1,13 @@ +fix typo that breaks compilation with Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- gapfiller-2.1.1/src/data_structures/Reads.cpp.orig 2017-04-06 13:30:10.978641815 +0200 ++++ gapfiller-2.1.1/src/data_structures/Reads.cpp 2017-04-06 13:38:39.941387943 +0200 +@@ -154,7 +154,7 @@ + case 1: out.append("C"); break; + case 2: out.append("G"); break; + case 3: out.append("T"); break; +- default: cout << "strange "<< cout << "\n"; ++ default: cout << "strange " << out << "\n"; + } + } + -- GitLab From 1730f76e147bfacab9a328311e2dce727c617736 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:48:15 +0200 Subject: [PATCH 717/818] adding easyconfigs: fqtrim-0.9.5-intel-2017a.eb --- .../f/fqtrim/fqtrim-0.9.5-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb new file mode 100644 index 0000000000..c00d6cd413 --- /dev/null +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'fqtrim' +version = '0.9.5' + +homepage = 'http://ccb.jhu.edu/software/fqtrim/' +description = """fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, + terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing + machines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] +sources = [SOURCE_TAR_GZ] + +buildopts = 'release CC="$CXX" LINKER="$CXX"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 799702c12e239d7de2a423c2730bbb120bdbc92a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 16:16:56 +0200 Subject: [PATCH 718/818] adding easyconfigs: DBG2OLC-20170208-intel-2017a.eb --- .../d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb new file mode 100644 index 0000000000..367145a273 --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c827dba5e6c5962a872c23d29dc191513a343168 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 16:03:20 +0000 Subject: [PATCH 719/818] Add --enable-fortran-calling-convention=gfortran to Octave eb. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index e845e9c89e..534dc92f99 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -52,6 +52,8 @@ configopts += 'UIC=$EBROOTQT5/bin/uic ' configopts += 'RCC=$EBROOTQT5/bin/rcc ' configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From 4d1e8dcd8cac962fd799d7c7abd261952559ddef Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 7 Apr 2017 08:55:29 +0200 Subject: [PATCH 720/818] Update METIS-5.1.0-foss-2016b.eb Needed for OpenFOAM # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb index 1510375706..56000b7259 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + builddependencies = [('CMake', '3.6.1')] configopts = ['', 'shared=1'] -- GitLab From 18cb49ea57b2f04daf6f925cb00e2f9101bd260f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Apr 2017 09:28:35 +0100 Subject: [PATCH 721/818] adding easyconfigs: gnuplot-5.0.5-foss-2016b.eb --- .../g/gnuplot/gnuplot-5.0.5-foss-2016b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100755 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb new file mode 100755 index 0000000000..52cec88efd --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.5' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.26'), + ('libgd', '2.2.3'), + ('Pango', '1.40.3'), + ('libcerf', '1.5'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From a38d10acbf7234f434e0c19ff59dc699bc1f57d4 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 10 Apr 2017 10:54:07 +0200 Subject: [PATCH 722/818] Stacks 1.45 build with the foss-2016a toolchain. --- .../s/Stacks/Stacks-1.45-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb new file mode 100644 index 0000000000..4f24751d68 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.45' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 21dee843cc0e8baa54067ef32a50cd458268bc25 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:27:16 +0200 Subject: [PATCH 723/818] Add Qt5/5.8 for intel/2017a --- .../pkg-config-0.29.2-intel-2017a.eb | 27 +++++++++++++++ .../q/Qt5/Qt5-5.8.0-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb new file mode 100644 index 0000000000..90af56a5b1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb new file mode 100644 index 0000000000..fc41f1c1fd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.8.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['Qt5-5.7.1_fix-nan-inf.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), #, '', ('GCCcore', '6.3.0')), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From 9406dda37ebe8a116f962078b11b46179fe977e7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:28:50 +0200 Subject: [PATCH 724/818] Added ParaView-5.3.0-intel-2017a-mpi --- .../c/CMake/CMake-3.7.2-intel-2017a.eb | 31 +++++++++++ .../h/HDF5/HDF5-1.8.18-intel-2017a.eb | 26 ++++++++++ .../ParaView-5.3.0-intel-2017a-mpi.eb | 52 +++++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb new file mode 100644 index 0000000000..d78b6b43f1 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb new file mode 100644 index 0000000000..570e4a8ff2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb new file mode 100644 index 0000000000..a124946808 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.3.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), + ('zlib', '1.2.11'), + ('HDF5', '1.8.18'), + ('Python', '2.7.13'), +] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 1f1e58d79e385169568b49542262db25ac27c804 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:37:48 +0200 Subject: [PATCH 725/818] Added CGAL-4.9-intel-2017a-Python-2.7.13 --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 36 ++++ .../e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb | 13 ++ .../m/MPFR/MPFR-3.1.5-20161219.patch | 174 ++++++++++++++++++ .../m/MPFR/MPFR-3.1.5-intel-2017a.eb | 29 +++ 4 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9b23706bf9 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.5'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..86af55ba48 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch new file mode 100644 index 0000000000..6b2d11466e --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch @@ -0,0 +1,174 @@ +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb new file mode 100644 index 0000000000..94a6262015 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.5' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + 'MPFR_ictce_remove-deprecated-mp.patch', + '%(name)s-%(version)s-20161219.patch', +] + +dependencies = [('GMP', '6.1.2')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 7c2309cf46942ad0342bc4102db6e55fd02cef94 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:40:35 +0200 Subject: [PATCH 726/818] Added OpenFOAM-4.1-intel-2017a --- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 25 ++ .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 339 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 36 ++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb | 18 + 4 files changed, 418 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb new file mode 100644 index 0000000000..352a974db9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -0,0 +1,25 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.7.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch new file mode 100644 index 0000000000..6c5fc1671a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -0,0 +1,339 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -41,7 +41,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPV3blockMeshReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -42,7 +42,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPV3FoamReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -16,7 +16,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVReaders + PVblockMeshReader/Allwmake $* +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -42,7 +42,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPVblockMeshReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -43,7 +43,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPVFoamReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=$(cd ${BASH_SOURCE%/*/*/*} && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools 2017-04-10 14:51:01.473221230 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4.1/etc/config.sh/metis +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/metis 2017-04-10 14:51:01.473221230 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi OpenFOAM-4.x-version-4.1/etc/config.sh/mpi +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/mpi 2017-04-10 14:51:01.473221230 +0200 +@@ -249,6 +249,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-version-4.1/etc/config.sh/paraview +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version-4.1/etc/config.sh/scotch +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/scotch 2017-04-10 14:51:01.473221230 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-version-4.1/etc/config.sh/settings +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/settings 2017-04-10 14:51:01.473221230 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb new file mode 100644 index 0000000000..214d84ba90 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '4.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['318a446c4ae6366c7296b61184acd37c'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '7.0'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.4'), + ('CGAL', '4.9', '-Python-2.7.13'), + ('ParaView', '5.3.0', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.7.2'), + ('flex', '2.6.3'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb new file mode 100644 index 0000000000..56f2a3c362 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' -- GitLab From f0c6c952907f6b57aaef620f887e0e90aabd9940 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:47:12 +0200 Subject: [PATCH 727/818] Downgrade ParaView to 5.2 as OpenFOAM 4.1 does not work with 5.3 They uses something that has been dropped in ParaView 5.3 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 2 +- ...3.0-intel-2017a-mpi.eb => ParaView-5.2.0-intel-2017a-mpi.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/ParaView/{ParaView-5.3.0-intel-2017a-mpi.eb => ParaView-5.2.0-intel-2017a-mpi.eb} (99%) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index 214d84ba90..2469f2947a 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.9', '-Python-2.7.13'), - ('ParaView', '5.3.0', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb similarity index 99% rename from easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb rename to easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index a124946808..addfba2c58 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ParaView' -version = '5.3.0' +version = '5.2.0' versionsuffix = '-mpi' homepage = "http://www.paraview.org" -- GitLab From 9f863dc507b877ed77968f9d56a47408b7f5e970 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 11 Apr 2017 10:33:06 +0200 Subject: [PATCH 728/818] Switch OpenFOAM 4.1 to Qt 4.x OpenFOAM doesn't work with Qt5 yet... --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 48 ------------------- .../ParaView-5.2.0-intel-2017a-mpi.eb | 4 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb | 28 +++++++++++ 4 files changed, 31 insertions(+), 51 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index 9b23706bf9..da60ff72f0 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('MPFR', '3.1.5'), ('GMP', '6.1.2'), ('libGLU', '9.0.0'), - ('Qt5', '5.8.0'), + ('Qt', '4.8.7'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch index 6c5fc1671a..1098db34cb 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -20,30 +20,6 @@ diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/s fi wmake -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -41,7 +41,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPV3blockMeshReaderPanel -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -42,7 +42,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPV3FoamReaderPanel diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake --- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-10-16 16:11:45.000000000 +0200 +++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2017-04-10 14:51:01.472221220 +0200 @@ -56,30 +32,6 @@ diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/grap wmake $targetType vtkPVReaders PVblockMeshReader/Allwmake $* -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -42,7 +42,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPVblockMeshReaderPanel -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -43,7 +43,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPVFoamReaderPanel diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc --- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 +++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index addfba2c58..903174f12f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -18,7 +18,7 @@ dependencies = [ ('X11', '20170314'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), - ('Qt5', '5.8.0'), + ('Qt', '4.8.7'), ('zlib', '1.2.11'), ('HDF5', '1.8.18'), ('Python', '2.7.13'), @@ -43,7 +43,7 @@ configopts += '-DBUILD_TESTING=OFF ' # Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +configopts += ' -DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$EBROOTQT/bin/qmake ' # The ParaView server can be cranky, test downloads are quite often failing, especially in the case # of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the # first serial attempt would fail. diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb new file mode 100644 index 0000000000..f45873187d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From 090054ad90088e311860cfdc0b1c228030fe1834 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 11 Apr 2017 12:51:58 +0200 Subject: [PATCH 729/818] Force usage of C++98 for Qt4 with intel/2017a --- easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb index f45873187d..f9818f430a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -5,6 +5,7 @@ homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++98'} source_urls = [ 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', -- GitLab From 18dd07b9caed0bb7fe11b96ec455336759009e7b Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Tue, 11 Apr 2017 11:10:43 -0400 Subject: [PATCH 730/818] Added PLINK-1.9b_4.1-x86_64.eb --- .../p/PLINK/PLINK-1.9b_4.1-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb new file mode 100644 index 0000000000..fdc904389a --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.9b-4.1-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['plink_linux_x86_64.zip'] +source_urls = ['https://www.cog-genomics.org/static/bin/plink170330/'] + +checksums = ['27e05daa4de39a15a9c7034998a35cc4'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 798ff8c32a5f67ca08f3607017b8b43ef4a3c9d5 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Tue, 11 Apr 2017 13:09:51 -0400 Subject: [PATCH 731/818] Corrected version name --- easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb index fdc904389a..1454e1f498 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -1,7 +1,7 @@ easyblock = 'PackedBinary' name = 'PLINK' -version = '1.9b-4.1-x86_64' +version = '1.9b_4.1-x86_64' homepage = 'https://www.cog-genomics.org/plink/1.9/' description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' -- GitLab From f2ad640fea6d4242d77456cb3899a1655a0bc73e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 12 Apr 2017 09:08:20 +0200 Subject: [PATCH 732/818] R extension nloptr need the NLopt lib --- .../n/NLopt/NLopt-2.4.2-intel-2017a.eb | 26 +++++++++++++++++++ .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 1 + 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb new file mode 100644 index 0000000000..a614e1864e --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 7c666ff2ec..963e074572 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -43,6 +43,7 @@ dependencies = [ ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal ('PROJ', '4.9.3'), # for rgdal ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), -- GitLab From e632d08a417cf5d687a4bfae93373ebc5ba6652b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 12 Apr 2017 09:16:03 +0200 Subject: [PATCH 733/818] Build shared lib for NLopt --- easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb index a614e1864e..607bdc3f75 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://ab-initio.mit.edu/nlopt/'] sources = [SOURCELOWER_TAR_GZ] +configopts = '--enable-shared' + sanity_check_paths = { 'files': ["lib/libnlopt.a", "include/nlopt.h"], 'dirs': [""], -- GitLab From bf0d8f6148716a4b0c12bb67c20d7d189527fb40 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 13 Apr 2017 06:32:52 +0930 Subject: [PATCH 734/818] New easyconfig for BioKanga 4.3.5 --- .../b/BioKanga/BioKanga-4.3.5-foss-2015b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb new file mode 100644 index 0000000000..c614af140d --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.5' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From eef18915f6321f45c5224f19fddb5cc35db4db51 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 10:42:59 +0800 Subject: [PATCH 735/818] adding easyconfigs: atomate-0.4.4-intel-2017a-Python-2.7.13.eb, custodian-1.1.0-intel-2017a-Python-2.7.13.eb, FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb, Flask-0.12-intel-2017a-Python-2.7.13.eb, Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb, gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb, Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb, matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb, monty-0.9.6-intel-2017a-Python-2.7.13.eb, mpmath-0.19-intel-2017a-Python-2.7.13.eb, pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb, pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb, pymongo-3.4.0-intel-2017a-Python-2.7.13.eb, PyYAML-3.12-intel-2017a-Python-2.7.13.eb, requests-2.13.0-intel-2017a-Python-2.7.13.eb, smoqe-0.1.3-intel-2017a-Python-2.7.13.eb, spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb, sympy-1.0-intel-2017a-Python-2.7.13.eb, Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb --- ...atomate-0.4.4-intel-2017a-Python-2.7.13.eb | 28 ++++++++++++ ...stodian-1.1.0-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ ...reWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 31 +++++++++++++ ...aginate-0.4.5-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++ .../Flask-0.12-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ ...nicorn-19.7.1-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ .../Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ ...plotlib-2.0.0-intel-2017a-Python-2.7.13.eb | 44 +++++++++++++++++++ .../monty-0.9.6-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ .../mpmath-0.19-intel-2017a-Python-2.7.13.eb | 34 ++++++++++++++ .../PyYAML-3.12-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++ ...tgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 29 ++++++++++++ ...ymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 32 ++++++++++++++ ...pymongo-3.4.0-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ ...quests-2.13.0-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ .../smoqe-0.1.3-intel-2017a-Python-2.7.13.eb | 25 +++++++++++ ...thon-1.9.9.38-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ .../sympy-1.0-intel-2017a-Python-2.7.13.eb | 33 ++++++++++++++ ...rkzeug-0.12.1-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ 19 files changed, 534 insertions(+) create mode 100644 easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6a33cf7fb2 --- /dev/null +++ b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'atomate' +version = '0.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pythonhosted.org/atomate/' +description = """atomate has implementations of FireWorks workflows for Materials Science.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('FireWorks', '1.4.2', versionsuffix), + ('custodian', '1.1.0', versionsuffix), + ('pymatgen', '4.7.3', versionsuffix), + ('pymatgen-db', '0.6.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..45b7389451 --- /dev/null +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'custodian' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/custodian' +description = """A simple JIT job management framework in Python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('monty', '0.9.6', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..526b35054c --- /dev/null +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'FireWorks' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/FireWorks' +description = """FireWorks helps run calculation workflows, with a centralized workflow server + controlling many worker nodes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Flask', '0.12', versionsuffix), + ('Flask-paginate', '0.4.5', versionsuffix), + ('PyYAML', '3.12', versionsuffix), + ('gunicorn', '19.7.1', versionsuffix), + ('monty', '0.9.6', versionsuffix), + ('pymongo', '3.4.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..153e1028fe --- /dev/null +++ b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'Flask-paginate' +version = '0.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Flask-paginate" +description = """Simple paginate support for flask.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_ZIP] + +dependencies = [ + ('Python', '2.7.13'), + ('Flask', '0.12', versionsuffix), +] + +options = {'modulename': 'flask_paginate'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b305d04f47 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'Flask' +version = '0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Flask" +description = """A microframework based on Werkzeug, Jinja2 and good intentions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Jinja2', '2.9.6', versionsuffix), + ('Werkzeug', '0.12.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6e2be6854a --- /dev/null +++ b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'gunicorn' +version = '19.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/gunicorn" +description = """WSGI HTTP Server for UNIX.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..0069b2587c --- /dev/null +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'Jinja2' +version = '2.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Jinja2" +description = """A small but fast and easy to use stand-alone template engine written in pure python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4cff5e718d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1'), + ('libpng', '1.6.29'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..64c36ac39f --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'monty' +version = '0.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/monty/" +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..db5a0e5289 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '0.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.13')] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4ff041f5c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('libyaml', '0.1.7'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..908d8b8ff5 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'pymatgen-db' +version = '0.6.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymatgen-db' +description = """Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen) + materials analysis library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pymatgen', '4.7.3', versionsuffix), + ('smoqe', '0.1.3', versionsuffix), +] + +options = {'modulename': 'matgendb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..f8b263a2dd --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pymatgen' +version = '4.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('matplotlib', '2.0.0', versionsuffix), + ('monty', '0.9.6', versionsuffix), + ('mpmath', '0.19', versionsuffix), + ('requests', '2.13.0', versionsuffix), + ('spglib-python', '1.9.9.38', versionsuffix), + ('sympy', '1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9bb19f1090 --- /dev/null +++ b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pymongo' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymongo' +description = """Python driver for MongoDB.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..786bbdf2c6 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..a5ff78eb95 --- /dev/null +++ b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'smoqe' +version = '0.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/smoqe' +description = """Simple MongoDB Query Engine (SMoQE).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pymongo', '3.4.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6c2b70d3f7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.9.9.38' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..444574067c --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# patch to fix tests +patches = ['sympy-1.0_tests-unicode.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('mpmath', '0.19', '-Python-%(pyver)s'), +] + +# runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9f007d3773 --- /dev/null +++ b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'Werkzeug' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/WerkZeug" +description = """The Swiss Army knife of Python web development.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From e64a152e2eba52d015850c2cf549afd467ca0f49 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 11:18:23 +0800 Subject: [PATCH 736/818] use existing libyaml with dummy toolchain --- .../p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb index 4ff041f5c0..73b6477407 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), - ('libyaml', '0.1.7'), + ('libyaml', '0.1.7', '', True), ] options = {'modulename': 'yaml'} -- GitLab From 23807849f1af83d3d0520249a6694f0317f8515f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 13:13:48 +0800 Subject: [PATCH 737/818] remove libpng from matplotlib dependencies (already a dependency of freetype) --- .../m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb index 4cff5e718d..e00702b768 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -17,7 +17,6 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.13'), ('freetype', '2.7.1'), - ('libpng', '1.6.29'), ] exts_list = [ -- GitLab From 86b92838f0b3009d1ec12ffc53e2b7f6993d0974 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Apr 2017 10:20:31 +0100 Subject: [PATCH 738/818] Fix libpng version conflict --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb index 52cec88efd..20416b1946 100755 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb @@ -25,7 +25,7 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] dependencies = [ ('cairo', '1.14.6'), ('libjpeg-turbo', '1.5.0'), - ('libpng', '1.6.26'), + ('libpng', '1.6.24'), ('libgd', '2.2.3'), ('Pango', '1.40.3'), ('libcerf', '1.5'), -- GitLab From 08e498cb5cc4bf318ed4660616330eb391c4b42c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 11:49:10 +0200 Subject: [PATCH 739/818] adding easyconfigs: bx-python-0.7.4-intel-2017a-Python-2.7.13.eb, LZO-2.10-intel-2017a.eb --- ...-python-0.7.4-intel-2017a-Python-2.7.13.eb | 47 +++++++++++++++++++ .../easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb | 31 ++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8f02847ea1 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'bx-python' +version = '0.7.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + + +dependencies = [ + ('Python', '2.7.13'), + ('LZO', '2.10'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " + +exts_list = [ + ('python-lzo', '1.11', { + 'modulename': 'lzo', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], + 'source_tmpl': 'python-lzo-%(version)s.tar.gz', + }), + (name, version, { + 'modulename': 'bx', + 'source_urls': ['https://github.com/bxlab/bx-python/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb new file mode 100644 index 0000000000..801057a84f --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage + 'download/'] + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' -- GitLab From ffa2d8c231fe75d6527db2440b07d8f50b250975 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 13:14:06 +0200 Subject: [PATCH 740/818] {math}[intel/2016b] scipy 0.19.0 + numpy 1.12.1 w/ Python 3.5.2 --- .../n/numpy/numpy-1.12.0-mkl.patch | 55 +++++++++++++++++++ .../numpy-1.12.1-intel-2016b-Python-3.5.2.eb | 23 ++++++++ .../scipy-0.19.0-intel-2016b-Python-3.5.2.eb | 19 +++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch new file mode 100644 index 0000000000..3d09924f96 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..b83a080a7d --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +patches = ['numpy-1.12.0-mkl.patch'] + +dependencies = [ + ('Python', '3.5.2'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..523cf018d9 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.19.0' +versionsuffix = '-Python-3.5.2' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('numpy', '1.12.1', versionsuffix), +] + +moduleclass = 'math' -- GitLab From e085c578bfb1eac166f793d1b1877a36059d0491 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 13:17:35 +0200 Subject: [PATCH 741/818] adding easyconfigs: Stacks-1.46-intel-2017a.eb, sparsehash-2.0.3-intel-2017a.eb --- .../s/Stacks/Stacks-1.46-intel-2017a.eb | 35 +++++++++++++++++++ .../sparsehash-2.0.3-intel-2017a.eb | 23 ++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb new file mode 100644 index 0000000000..341b4db710 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.46' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '1.4'), + ('sparsehash', '2.0.3'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb new file mode 100644 index 0000000000..32f208ded5 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.3' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """An extremely memory-efficient hash_map + implementation. 2 bits/entry overhead! The SparseHash library + contains several hash-map implementations, including + implementations that optimize for space or speed.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/sparsehash/sparsehash/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 28cf85302f91dcc01e4e373f8d7a8b84ee9a0aff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 10:08:35 +0200 Subject: [PATCH 742/818] adding easyconfigs: MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb, Eigen-3.2.10-intel-2016b.eb --- ...MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bfa4a70408 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'MRtrix' +version = '0.3.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), + ('Qt', '4.8.7'), + ('Eigen', '3.2.10'), +] + +moduleclass = 'bio' -- GitLab From 3ce4bc6da6754819d8706ff8d011551ddc02dbfc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 19 Apr 2017 13:03:43 +0200 Subject: [PATCH 743/818] Add CUDA/8.0.61 --- .../c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..02ed53d7d5 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '8.0.61' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] + +sources = ['cuda_%(version)s_375.26_linux-run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb new file mode 100644 index 0000000000..b3ad585f70 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '8.0.61' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] + +sources = ['cuda_%(version)s_375.26_linux-run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' -- GitLab From 8307b771d0e3d26a65a442d1e3c761ccb7bdb934 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 19 Apr 2017 13:14:31 +0200 Subject: [PATCH 744/818] Drop Cuda easyconfig with unsupported GCC --- .../c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb deleted file mode 100644 index 02ed53d7d5..0000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'CUDA' -version = '8.0.61' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'GCCcore', 'version': '6.3.0'} - -source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] - -sources = ['cuda_%(version)s_375.26_linux-run'] - -modextravars = {'CUDA_HOME': '%(installdir)s'} - -moduleclass = 'system' -- GitLab From ad01055ce5e98a5dce7f62d59d7bfd360355cf18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:53:42 +0200 Subject: [PATCH 745/818] adding easyconfigs: JasPer-1.900.1-intel-2017a.eb --- .../j/JasPer/JasPer-1.900.1-intel-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb new file mode 100644 index 0000000000..80e537b9bb --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 98c8fa75eab423831af2b64676302a7ab477997f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:54:13 +0200 Subject: [PATCH 746/818] adding easyconfigs: makedepend-1.0.5-GCCcore-6.3.0.eb, xorg-macros-1.19.1-GCCcore-6.3.0.eb, xproto-7.0.31-GCCcore-6.3.0.eb --- .../makedepend-1.0.5-GCCcore-6.3.0.eb | 26 +++++++++++++++++ .../xorg-macros-1.19.1-GCCcore-6.3.0.eb | 27 +++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 29 +++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb create mode 100755 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b7d5d70c2d --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_UTIL_SOURCE] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb new file mode 100755 index 0000000000..6f48acb154 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.1' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('Autotools', '20150215'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..06e2a620f7 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From e4c9596d4b47c878879c7413a42508d5bd897b29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:58:21 +0200 Subject: [PATCH 747/818] adding easyconfigs: cURL-7.54.0-GCCcore-6.3.0.eb --- .../c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..8d7f087e2b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.54.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From a38dd1652faef8092f063cfcb4a8f8c95aaa21a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:27:11 +0200 Subject: [PATCH 748/818] adding easyconfigs: UDUNITS-2.2.24-intel-2017a.eb --- .../u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb new file mode 100644 index 0000000000..0e89a4b4d6 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +dependencies = [('expat', '2.2.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' -- GitLab From b1b868b9fad00772a8c991df2a84b5e91e4488e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:27:39 +0200 Subject: [PATCH 749/818] adding easyconfigs: HDF-4.2.12-intel-2017a.eb --- .../h/HDF/HDF-4.2.12-intel-2017a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb new file mode 100644 index 0000000000..36b03f1853 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.12' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), + ('libjpeg-turbo', '1.5.1'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' -- GitLab From db59e7eca44753a4e802ccff209fe89a4804e19d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:28:06 +0200 Subject: [PATCH 750/818] adding easyconfigs: g2lib-1.4.0-intel-2017a.eb, g2clib-1.6.0-intel-2017a.eb --- .../g/g2clib/g2clib-1.6.0-intel-2017a.eb | 17 +++++++++++++++ .../g/g2lib/g2lib-1.4.0-intel-2017a.eb | 21 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb new file mode 100644 index 0000000000..91bbbfa89b --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb @@ -0,0 +1,17 @@ +name = 'g2clib' +version = '1.6.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] + +dependencies = [('JasPer', '1.900.1')] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb new file mode 100644 index 0000000000..c7f92d0e2b --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'g2lib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] + +patches = ['fix_makefile.patch'] + +dependencies = [('JasPer', '1.900.1')] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fpp -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' -- GitLab From 766e37c4509ed9d8de231878b0b1080dc2922fd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:47:38 +0200 Subject: [PATCH 751/818] {geo}[intel/2017a] ESMF 6.3.0rp1 --- .../e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb | 31 +++++++++++++++++++ .../ESMF-6.3.0rp1_fix-file-open-test.patch | 13 ++++++++ .../netCDF-C++4-4.3.0-intel-2017a.eb | 24 ++++++++++++++ 3 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb new file mode 100644 index 0000000000..fec7e0e3f7 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '6.3.0rp1' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'ESMF-6.1.1_libopts.patch', + 'ESMF-%(version)s_fix-file-open-test.patch', +] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('netCDF-C++4', '4.3.0'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch new file mode 100644 index 0000000000..62a98e0354 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch @@ -0,0 +1,13 @@ +fix compilation issue with recent compilers +cfr. https://sourceforge.net/p/esmf/esmf/ci/3706bf758012daebadef83d6575c477aeff9c89b/#diff-1 +--- src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp.orig 2017-04-19 13:44:03.384547426 +0200 ++++ src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp 2017-04-19 13:44:16.864674576 +0200 +@@ -105,7 +105,7 @@ + ReadABAQUS::~ReadABAQUS() + { + mdbImpl->release_interface(readMeshIface); +- if (NULL != abFile) ++ if (abFile.is_open()) + abFile.close(); + } + diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb new file mode 100644 index 0000000000..959f14667b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 4133ea658c683e1f2a46a28bb5494b71aa9765e1 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 19 Apr 2017 15:32:06 +0200 Subject: [PATCH 752/818] v6.0 --- .../c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb new file mode 100644 index 0000000000..942648ea47 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '6.0' +cuda_version = '8.0.61' + +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-8.0-linux-x64-v%(version)s.tgz'] + +dependencies = [('CUDA', cuda_version)] + +checksums = [ + '4aacb7acb93c5e4dfa9db814df496219', # cudnn-8.0-linux-x64-v6.0.tgz, Jan 20 2017 download +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' -- GitLab From 695590ab4dad6e11621fcf63d0bf7152afc9ad9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 18:36:20 +0200 Subject: [PATCH 753/818] adding easyconfigs: libiconv-1.15-intel-2017a.eb --- .../l/libiconv/libiconv-1.15-intel-2017a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb new file mode 100644 index 0000000000..fb6be42e9f --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.15' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' -- GitLab From 2d502840969e2356078da89e05ac197c67ae0306 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:14:45 +0200 Subject: [PATCH 754/818] install libiconv with GCCcore rather than intel toolchain --- ...nv-1.15-intel-2017a.eb => libiconv-1.15-GCCcore-6.3.0.eb} | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/l/libiconv/{libiconv-1.15-intel-2017a.eb => libiconv-1.15-GCCcore-6.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb similarity index 75% rename from easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb rename to easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index fb6be42e9f..c2a203f1b2 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -6,11 +6,14 @@ version = '1.15' homepage = 'https://www.gnu.org/software/libiconv' description = "Libiconv converts from one character encoding to another through Unicode conversion" -toolchain = {'name': 'intel', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], -- GitLab From b72075148a92dc4187d739278cb11f5f33e40709 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:35:46 +0200 Subject: [PATCH 755/818] adding easyconfigs: numba-0.32.0-intel-2017a-Python-2.7.13.eb --- .../numba-0.32.0-intel-2017a-Python-2.7.13.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..dc868ad142 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.32.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('LLVM', '4.0.0'), +] + +exts_list = [ + ('llvmlite', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' -- GitLab From bf7342099c04a56d0715d02cdf2531ee57e1d194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:58:08 +0200 Subject: [PATCH 756/818] adding easyconfigs: PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb, ZeroMQ-4.2.2-intel-2017a.eb, OpenPGM-5.2.122-intel-2017a.eb, libsodium-1.0.12-intel-2017a.eb --- .../libsodium/libsodium-1.0.12-intel-2017a.eb | 20 +++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb | 30 ++++++++++++++++ ...Q-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb | 30 ++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb | 36 +++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb new file mode 100644 index 0000000000..faf9cf93a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.12' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb new file mode 100644 index 0000000000..d604042523 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] + +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb new file mode 100644 index 0000000000..3ee565a8d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.2' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +dependencies = [ + ('Python', '2.7.13'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb new file mode 100644 index 0000000000..165ba15944 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['52499909b29604c1e47a86f1cb6a9115'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.29.2'), + ('libsodium', '1.0.12'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 54c21ef39805e3658819582f56a821f29ea5b96c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:58:44 +0200 Subject: [PATCH 757/818] adding easyconfigs: GSL-2.3-intel-2017a.eb --- .../easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb new file mode 100644 index 0000000000..23a2fed6dc --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From 5611e1be3e27234852c0429f2a98458f8e3a0e2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 11:42:16 +0200 Subject: [PATCH 758/818] add patch to avoid configparser declaring ownership of backports namespace, fixes #3825 --- ...igparser-3.5.0-foss-2016a-Python-2.7.11.eb | 16 +++------- ...gparser-3.5.0-intel-2016b-Python-2.7.12.eb | 15 ++------- ...igparser-3.5.0-intel-2016b-Python-3.5.2.eb | 7 ++--- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 4 files changed, 41 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb index 8172078525..f9db925788 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb @@ -12,26 +12,18 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '2.7.11'), -] -builddependencies = [ - ('pip', '8.1.2', versionsuffix), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.11')] +builddependencies = [('pip', '8.1.2', versionsuffix)] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], } -# XXX: hack! for some reason the sanity check imports fail, even though the -# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py -# in backports makes it pass and hopefully does not break anything. -postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb index 10fc576297..bed63bcc08 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb @@ -12,26 +12,17 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '2.7.12'), -] -builddependencies = [ - ('pip', '8.1.2', versionsuffix), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.12')] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], } -# XXX: hack! for some reason the sanity check imports fail, even though the -# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py -# in backports makes it pass and hopefully does not break anything. -postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb index e3bb6d9e20..113e88c75f 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb @@ -12,12 +12,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '3.5.2'), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '3.5.2')] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From cf19458b143e485f7f38567676fccbce91806cd1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 17:12:07 +0200 Subject: [PATCH 759/818] re-add nbconvert extension in IPython easyconfigs --- ...igparser-3.5.0-foss-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ ...rypoints-0.2.2-foss-2016b-Python-2.7.12.eb | 28 +++++++++++++++++ .../IPython-5.1.0-foss-2016b-Python-2.7.12.eb | 12 +++---- ...IPython-5.1.0-intel-2016b-Python-2.7.12.eb | 12 +++---- ...IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 16 +++++----- 5 files changed, 75 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5bd3d25aab --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'configparser' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://docs.python.org/3/library/configparser.html' +description = "configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] +sources = ['configparser-%(version)s.tar.gz'] + +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.12')] + +use_pip = True + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], +} + +sanity_check_commands = [ + ('python', "-c 'import configparser'"), + ('python', "-c 'from backports import configparser'"), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a82113c472 --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'entrypoints' +version = '0.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/takluyver/entrypoints' +description = """Entry points are a way for Python packages to advertise objects with some common interface.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('configparser', '3.5.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/entrypoints.py'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb index 15948e83d4..ec7c04c10b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -114,11 +112,9 @@ exts_list = [ ('pexpect', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '4.2.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('nbconvert', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb index 73b84816cd..ad14e82e32 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -114,11 +112,9 @@ exts_list = [ ('pexpect', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '4.2.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('nbconvert', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index 89001fc17a..01c5f93a20 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '10.1', versionsuffix), ('prompt-toolkit', '1.0.13', versionsuffix), ] @@ -111,11 +109,13 @@ exts_list = [ ('pexpect', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '5.1.1', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), -- GitLab From f142dcdf9ad525403d586d37b3bf68d2a2933032 Mon Sep 17 00:00:00 2001 From: Basil Neff Date: Thu, 20 Apr 2017 17:31:03 +0200 Subject: [PATCH 760/818] Change source_urls of pycrypto to https://pypi.python.org/packages/source/p/pycrypto/: A crypto library should be downloaded via https, python.org seems more reliable than dlitz.net, dlitz.net is currently not online. --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb | 2 +- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb | 2 +- .../p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb | 2 +- 61 files changed, 61 insertions(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 0cacb5b908..6b56eb27c3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index c4b91910db..8b4e1559a2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index 6cb74160de..acd58a0881 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 2bf2b3c0c7..e8f04d3c24 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index d616f3a678..f6fb8098a2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 3bba96e78d..e63f73a086 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 5578abe094..007214e5b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 4289f275f3..8a60745ce6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index f16c276300..f9d52e68ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 7ca3e0d30a..b14cb9623b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 90aff56172..161e0d5c72 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 540888954b..236dc03eb2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index 500c945db9..61b2cea7f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 66287172c5..15781ef44b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index 49ed840807..92cc06cd43 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 4fa82a32c1..2bcf51b6e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -95,7 +95,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 36a33282cc..b4d230688e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb index ceffc4847a..f016ee6e7a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index 42a08985d0..7040853aa6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index ba6ada1467..0f7cc1242b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index f39ab1c056..8305709383 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb index 47c4558b9f..eb4f43f9dd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 8d585acc42..099f1ae1b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -86,7 +86,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index 9cf2d30627..b98190bc1b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 0d7187668b..6d47c29a41 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 1f04581f6c..5d62c714b3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index d6acb56cd0..466af1fc83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 0a6a82b9fe..9112593773 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 78b8331206..b74b1eef65 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index 8bc486f394..fa3597eb0f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index f91d5d9be1..74108af019 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 1589ad3044..7f83fbbc76 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index cc438001ba..d802876700 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 8a3b97a885..8d651bcfeb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -84,7 +84,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index ff8c4dd1f7..0ac840f64e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 400936afa7..8301c629cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 535df5f445..fcb554f578 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 15167c0da9..d08ab61505 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 5da8fad6cd..3479838d18 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index a19c3193df..e92ff5d69d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -84,7 +84,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index c42116cc9a..0f597d584c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index e020765a41..2963dc2fc7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 0e5c8bdaf5..6953cb6dbe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 50b5d85a22..0f287711fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 954cb1d6c9..77b75dd242 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 2117038315..3ba0f79c58 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index de0245d75a..58ac4915cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 39c33c3855..f324c5da55 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index dfd615f248..76e8491a9b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index 530b345146..e15e16e66c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -62,7 +62,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 1f4aa039b5..fbcadd2903 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -62,7 +62,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 85a061b4b2..aaa2d02a7e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 43f98bbf39..80c176feab 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index fa4d5db712..e220cd9cc4 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 7f32b2fbd5..1fe2eb4748 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 34b680443b..3794d8056b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index f17ad6e258..0ea37fde6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index bba87219ba..6b27ddc007 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -97,7 +97,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index 3034157afb..0f528e0158 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb index f40c4aab55..2fc712658f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb index 805061ab30..198569f10b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 2582246e9f15e21fffde3cf51c5c8e8f192422ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 20:47:44 +0200 Subject: [PATCH 761/818] adding easyconfigs: IPython-5.3.0-intel-2017a-Python-2.7.13.eb --- ...IPython-5.3.0-intel-2017a-Python-2.7.13.eb | 176 ++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..62ef063309 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,176 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2017.4.17', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('scandir', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('pexpect', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'patches': ['configparser-3.5.0_no-backports-namespace.patch'], + 'use_pip': True, + }), + ('entrypoints', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'source_tmpl': 'entrypoints-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('testpath', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/py2.py3/t/testpath/'], + 'source_tmpl': 'testpath-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'source_tmpl': 'wcwidth-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('prompt-toolkit', '1.0.14', { + 'modulename': 'prompt_toolkit', + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'source_tmpl': 'prompt_toolkit-%(version)s-py2-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), + ('ipykernel', '4.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('ipywidgets', '5.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' -- GitLab From d9723ff8ec091b57e3ffbf11566782a52a612a75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 21:05:59 +0200 Subject: [PATCH 762/818] adding easyconfigs: ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb, h5py-2.7.0-intel-2017a-Python-2.7.13.eb, pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb, pkg-config-0.29.2-GCCcore-6.3.0.eb --- .../h5py-2.7.0-intel-2017a-Python-2.7.13.eb | 32 +++++++ ...ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb | 88 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-6.3.0.eb | 32 +++++++ ...gconfig-1.2.2-intel-2017a-Python-2.7.13.eb | 26 ++++++ 4 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..300f1e3d6e --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.13'), + ('HDF5', '1.10.0-patch1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d74840fcf3 --- /dev/null +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,88 @@ +easyblock = 'Bundle' + +name = 'ipyrad' +version = '0.6.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipyrad.readthedocs.io' +description = """ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic + data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('h5py', '2.7.0', versionsuffix), + ('numba', '0.32.0', versionsuffix), + ('IPython', '5.3.0', versionsuffix), +] + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize'], + }), + ('alabaster', '0.7.10', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster'], + }), + ('Babel', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer'], + }), + ('docutils', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], + }), + ('Sphinx', '1.5.5', { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx'], + }), + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('jupyter', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter'], + }), + ('ipyparallel', '6.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipyparallel'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings'], + }), + ('html5lib', '0.999999999', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib'], + }), + ('bleach', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach'], + }), + ('jupyter-console', '5.1.0', { + 'modulename': 'jupyter_console', + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_console'], + 'source_tmpl': 'jupyter_console-%(version)s.tar.gz', + }), + ('qtconsole', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], + }), + ('futures', '3.1.1', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], + }), + (name, version, { + 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/ipyrad'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b75a0d85ea --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..0df86ffc84 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 0be93bb3b688cde0add034758905359998691a30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 22:04:24 +0200 Subject: [PATCH 763/818] add patch file for configparser as extension in IPython easyconfig --- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From 0c7c4f5c3d8938754cdf2229ab8aa6743d375d6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 23:28:04 +0200 Subject: [PATCH 764/818] add toyplot extension in ipyrad easyconfig file --- ...ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb | 26 +++++++++++++++++- .../Pillow-4.1.0-intel-2017a-Python-2.7.13.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb index d74840fcf3..ecce4b3046 100644 --- a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -10,14 +10,15 @@ description = """ipyrad is an interactive toolkit for assembly and analysis of r toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') dependencies = [ ('Python', '2.7.13'), ('h5py', '2.7.0', versionsuffix), ('numba', '0.32.0', versionsuffix), ('IPython', '5.3.0', versionsuffix), + ('Pillow', '4.1.0', versionsuffix), ] exts_list = [ @@ -69,6 +70,29 @@ exts_list = [ 'modulename': 'concurrent.futures', 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], }), + ('arrow', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/arrow'], + }), + ('colormath', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormath'], + }), + ('multipledispatch', '0.4.9', { + 'source_urls': ['https://pypi.python.org/packages/source/m/multipledispatch'], + }), + ('pypng', '0.0.18', { + 'modulename': 'png', + 'source_urls': ['https://pypi.python.org/packages/source/p/pypng'], + }), + ('olefile', '0.44', { + 'source_urls': ['https://pypi.python.org/packages/source/o/olefile'], + 'source_tmpl': 'olefile-%(version)s.zip', + }), + ('reportlab', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], + }), + ('toyplot', '0.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toyplot'], + }), (name, version, { 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], 'source_tmpl': '%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..f4cf66d2ef --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.7'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From 4dd8a3443ae8329b20a05bce182f2386c3053d9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 21 Apr 2017 13:14:18 +0200 Subject: [PATCH 765/818] Go 1.8.1 binary version --- easybuild/easyconfigs/g/Go/Go-1.8.1.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.8.1.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.8.1.eb b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb new file mode 100644 index 0000000000..07ab4f25c4 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.8.1' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} +moduleclass = 'compiler' -- GitLab From 321af123d5b5f5bb627e1e067dbf730af59b4816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Apr 2017 13:16:53 +0200 Subject: [PATCH 766/818] adding easyconfigs: ViennaRNA-2.3.5-intel-2017a.eb --- .../ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb new file mode 100644 index 0000000000..daafb8cd29 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.3.5' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 28d361d3ce47585509674f61b14a5027ac94a1dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Apr 2017 11:00:31 +0200 Subject: [PATCH 767/818] add checksum for ViennaRNA 2.3.5 source tarball --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb index daafb8cd29..fc2a6f62b8 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -25,6 +25,8 @@ toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] +checksums = ['4542120adae9b7abb605e2304c2a1326'] + # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory -- GitLab From 513967084fe5171105b83b20c0cc16466b84346b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 17:12:25 +0800 Subject: [PATCH 768/818] bundle most of the python packages as extensions --- ...stodian-1.1.0-intel-2017a-Python-2.7.13.eb | 9 ++++- ...reWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 33 +++++++++++++++--- ...aginate-0.4.5-intel-2017a-Python-2.7.13.eb | 27 --------------- .../Flask-0.12-intel-2017a-Python-2.7.13.eb | 26 -------------- ...nicorn-19.7.1-intel-2017a-Python-2.7.13.eb | 24 ------------- .../Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb | 24 ------------- .../monty-0.9.6-intel-2017a-Python-2.7.13.eb | 26 -------------- .../mpmath-0.19-intel-2017a-Python-2.7.13.eb | 34 ------------------- ...tgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 9 ++++- ...ymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 32 ++++++++++++++--- ...pymongo-3.4.0-intel-2017a-Python-2.7.13.eb | 24 ------------- ...quests-2.13.0-intel-2017a-Python-2.7.13.eb | 24 ------------- .../smoqe-0.1.3-intel-2017a-Python-2.7.13.eb | 25 -------------- .../sympy-1.0-intel-2017a-Python-2.7.13.eb | 33 ------------------ .../s/sympy/sympy-1.0_tests-unicode.patch | 23 ------------- ...rkzeug-0.12.1-intel-2017a-Python-2.7.13.eb | 24 ------------- 16 files changed, 72 insertions(+), 325 deletions(-) delete mode 100644 easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch delete mode 100644 easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 45b7389451..2a8be8856b 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -15,7 +15,14 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), - ('monty', '0.9.6', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index 526b35054c..0323b8f8c9 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -15,12 +15,35 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), - ('Flask', '0.12', versionsuffix), - ('Flask-paginate', '0.4.5', versionsuffix), ('PyYAML', '3.12', versionsuffix), - ('gunicorn', '19.7.1', versionsuffix), - ('monty', '0.9.6', versionsuffix), - ('pymongo', '3.4.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('Flask', '0.12', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], + }), + ('Flask-paginate', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], + 'source_tmpl': 'flask-paginate-%(version)s.zip', + 'modulename': 'flask_paginate', + }), + ('Jinja2', '2.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('Werkzeug', '0.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug/'], + }), + ('gunicorn', '19.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], + }), + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), + ('pymongo', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 153e1028fe..0000000000 --- a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Flask-paginate' -version = '0.4.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Flask-paginate" -description = """Simple paginate support for flask.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_ZIP] - -dependencies = [ - ('Python', '2.7.13'), - ('Flask', '0.12', versionsuffix), -] - -options = {'modulename': 'flask_paginate'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index b305d04f47..0000000000 --- a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Flask' -version = '0.12' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Flask" -description = """A microframework based on Werkzeug, Jinja2 and good intentions.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('Jinja2', '2.9.6', versionsuffix), - ('Werkzeug', '0.12.1', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 6e2be6854a..0000000000 --- a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'gunicorn' -version = '19.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/gunicorn" -description = """WSGI HTTP Server for UNIX.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 0069b2587c..0000000000 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Jinja2' -version = '2.9.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Jinja2" -description = """A small but fast and easy to use stand-alone template engine written in pure python.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 64c36ac39f..0000000000 --- a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'monty' -version = '0.9.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/monty/" -description = """Monty implements supplementary useful functions for Python that are not part of the standard library. - Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton - and cached_class, and many more.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index db5a0e5289..0000000000 --- a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Author: Adam Huffman -# adam.huffman@crick.ac.uk -# The Francis Crick Institute - -easyblock = 'PythonPackage' - -name = 'mpmath' -version = '0.19' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://mpmath.org/' -description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex - types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation - can be performed just as well at 10-digit or 1000-digit precision, with either real or complex - numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely - high precision work.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] -sources = ['%(version)s.tar.gz'] - -dependencies = [('Python', '2.7.13')] - -runtest = 'python -c "import mpmath; mpmath.runtests();"' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 908d8b8ff5..b7bde5299a 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -16,7 +16,14 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('pymatgen', '4.7.3', versionsuffix), - ('smoqe', '0.1.3', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('smoqe', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], + }), ] options = {'modulename': 'matgendb'} diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index f8b263a2dd..c011699956 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -17,11 +17,35 @@ dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ('matplotlib', '2.0.0', versionsuffix), - ('monty', '0.9.6', versionsuffix), - ('mpmath', '0.19', versionsuffix), - ('requests', '2.13.0', versionsuffix), ('spglib-python', '1.9.9.38', versionsuffix), - ('sympy', '1.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('Flask', '0.12', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], + }), + ('Flask-paginate', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], + 'source_tmpl': 'flask-paginate-%(version)s.zip', + 'modulename': 'flask_paginate', + }), + ('gunicorn', '19.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], + }), + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), + ('mpmath', '0.19', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('sympy', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 9bb19f1090..0000000000 --- a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pymongo' -version = '3.4.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/pymongo' -description = """Python driver for MongoDB.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 786bbdf2c6..0000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'requests' -version = '2.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/requests' -description = """Python http for humans.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index a5ff78eb95..0000000000 --- a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'smoqe' -version = '0.1.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/smoqe' -description = """Simple MongoDB Query Engine (SMoQE).""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('pymongo', '3.4.0', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 444574067c..0000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sympy' -version = '1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# patch to fix tests -patches = ['sympy-1.0_tests-unicode.patch'] - -dependencies = [ - ('Python', '2.7.13'), - ('mpmath', '0.19', '-Python-%(pyver)s'), -] - -# runtest = 'python setup.py test' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch deleted file mode 100644 index 87e12a3b40..0000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch +++ /dev/null @@ -1,23 +0,0 @@ -Fix for Unicode error that causes one of the tests to fail - -For reference, see -http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte -and http://nedbatchelder.com/text/unipain/unipain.html - -Patch created by: - -Adam Huffman -The Francis Crick Institute - -diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py ---- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 -+++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 -@@ -164,7 +164,7 @@ - except CalledProcessError as e: - raise CodeWrapError( - "Error while executing command: %s. Command output is:\n%s" % ( -- " ".join(command), e.output.decode())) -+ " ".join(command), e.output.decode('ascii', 'ignore'))) - if not self.quiet: - print(retoutput) - diff --git a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 9f007d3773..0000000000 --- a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Werkzeug' -version = '0.12.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/WerkZeug" -description = """The Swiss Army knife of Python web development.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' -- GitLab From 5cbbbd21c3081ec7f660939e08bb4e12b23b3063 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 18:05:52 +0800 Subject: [PATCH 769/818] restore erroneously deleted file --- .../s/sympy/sympy-1.0_tests-unicode.patch | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch new file mode 100644 index 0000000000..87e12a3b40 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -0,0 +1,23 @@ +Fix for Unicode error that causes one of the tests to fail + +For reference, see +http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte +and http://nedbatchelder.com/text/unipain/unipain.html + +Patch created by: + +Adam Huffman +The Francis Crick Institute + +diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py +--- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 ++++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 +@@ -164,7 +164,7 @@ + except CalledProcessError as e: + raise CodeWrapError( + "Error while executing command: %s. Command output is:\n%s" % ( +- " ".join(command), e.output.decode())) ++ " ".join(command), e.output.decode('ascii', 'ignore'))) + if not self.quiet: + print(retoutput) + -- GitLab From ce6e45a9eff79478f37e7e8dec137a229cd1c9bc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 18:12:09 +0800 Subject: [PATCH 770/818] use Bundle easyblock for easyconfigs with extensions --- .../custodian-1.1.0-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- .../FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- ...pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 15 ++++++++++----- .../pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- 4 files changed, 40 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 2a8be8856b..e8bf835f61 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'custodian' version = '1.1.0' @@ -9,22 +9,28 @@ description = """A simple JIT job management framework in Python.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('custodian', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], + }), ('monty', '0.9.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], }), ] +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index 0323b8f8c9..f776bdcadf 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'FireWorks' version = '1.4.2' @@ -10,17 +10,18 @@ description = """FireWorks helps run calculation workflows, with a centralized w toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('FireWorks', version, { + 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], + }), ('Flask', '0.12', { 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], }), @@ -46,6 +47,11 @@ exts_list = [ }), ] +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index b7bde5299a..007db0084d 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'pymatgen-db' version = '0.6.5' @@ -10,23 +10,28 @@ description = """Pymatgen-db is a database add-on for the Python Materials Genom toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('pymatgen', '4.7.3', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('pymatgen-db', '0.6.5', { + 'modulename': 'matgendb', + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], + }), ('smoqe', '0.1.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], }), ] -options = {'modulename': 'matgendb'} +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index c011699956..718deacce4 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'Bundle' name = 'pymatgen' version = '4.7.3' @@ -10,9 +10,6 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), @@ -20,6 +17,7 @@ dependencies = [ ('spglib-python', '1.9.9.38', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ @@ -40,6 +38,9 @@ exts_list = [ ('mpmath', '0.19', { 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], }), + ('pymatgen', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], + }), ('requests', '2.13.0', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), @@ -48,6 +49,11 @@ exts_list = [ }), ] +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] -- GitLab From 07ac52418a3dd86aaa411fb487e172b7c3ae50cb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 25 Apr 2017 15:51:57 +0200 Subject: [PATCH 771/818] {chem} [dummy] ORCA/4.0.0.2 --- .../o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb new file mode 100644 index 0000000000..c9312c4044 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -0,0 +1,38 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.0.0.2' + +openmpiversion = '2.0.2' +versionsuffix = '-OpenMPI-%s' % openmpiversion + +homepage = 'http://cec.mpg.de/forum/' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Download from https://cec.mpg.de/orcadownload/index.php +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), openmpiversion.replace('.', ''))] + +checksums = ['a5b8ecdd3d004af4bc8190c986f34e11'] + +dependencies = [('OpenMPI', openmpiversion, '-GCC-6.3.0-2.27')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 85190c2bda5be363fb61a927f39ffe2a9911b564 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:28:39 +0200 Subject: [PATCH 772/818] adding easyconfigs: IMB-4.1-foss-2017a.eb --- .../easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb new file mode 100644 index 0000000000..87a1fa9cc3 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-21_09-32-59 +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """ +The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point +and global communication operations for a range of message sizes. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' +buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'dirs': ['bin', 'doc'] +} + +moduleclass = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 17.94, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'IMB-4.1-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1238017, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492759974, + "total_memory": 128828, +}] -- GitLab From b65a2b6bb4c73feb566e0c2ffb9030263b588a14 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 21:49:46 +0200 Subject: [PATCH 773/818] adding easyconfigs: SIONlib-1.7.1-foss-2017a.eb, SIONlib-1.7.1-foss-2017a-tools.eb --- .../SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 70 +++++++++++++++++++ .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 64 +++++++++++++++++ 2 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb new file mode 100644 index 0000000000..7d3b72d93e --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -0,0 +1,70 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-35-15 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.1' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. This package provides a stripped-down + installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against a tool requiring + a different SIONlib version.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = ['sionlib-%(version)sl.tar.gz'] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] + +checksums = [ + 'bc2ed625cdf967815007e71e732f38d1', # sionlib-1.7.1l.tar.gz +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 8.34, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a-tools.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1955553, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493148914, + "total_memory": 128828, +}] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb new file mode 100644 index 0000000000..667807f3cc --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -0,0 +1,64 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-34-35 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.1' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. SIONlib provides different interfaces: + parallel access using MPI, OpenMP, or their combination, and sequential access for post-processing + utilities.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)s'] + +checksums = [ + '9d613055896af2792518d6e0cda02588', # sionlib-1.7.1.tar.gz +] + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['sioncom', 'siongen', 'sionser']], + 'dirs': [] +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 14.02, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 4336229, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493148875, + "total_memory": 128828, +}] -- GitLab From 7a5457b4666d8716ecdedc2417d645c451103a60 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 21:50:23 +0200 Subject: [PATCH 774/818] adding easyconfigs: OTF2-2.0-foss-2017a.eb --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb new file mode 100644 index 0000000000..7d56604ccc --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -0,0 +1,67 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-37-09 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz +] + +builddependencies = [('SIONlib', '1.7.1', '-tools')] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib/libotf2.a", "lib64/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 69.0, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'OTF2-2.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 19885165, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493149028, + "total_memory": 128828, +}] -- GitLab From 979674e2721a618799239d5ea2a795a9481e5aa6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 26 Apr 2017 08:47:16 +0800 Subject: [PATCH 775/818] reorder extensions --- .../custodian-1.1.0-intel-2017a-Python-2.7.13.eb | 6 +++--- .../FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 6 +++--- .../pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 6 +++--- .../pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 9 +++------ 4 files changed, 12 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index e8bf835f61..0c065c7d55 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -18,12 +18,12 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('custodian', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], - }), ('monty', '0.9.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], }), + ('custodian', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index f776bdcadf..ac5fcef9e1 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -19,9 +19,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('FireWorks', version, { - 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], - }), ('Flask', '0.12', { 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], }), @@ -45,6 +42,9 @@ exts_list = [ ('pymongo', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], }), + ('FireWorks', version, { + 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 007db0084d..7c6022d3f6 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -19,13 +19,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ + ('smoqe', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], + }), ('pymatgen-db', '0.6.5', { 'modulename': 'matgendb', 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], }), - ('smoqe', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], - }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index 718deacce4..86166ed4e4 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -38,15 +38,12 @@ exts_list = [ ('mpmath', '0.19', { 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], }), - ('pymatgen', version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], - }), - ('requests', '2.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), ('sympy', '1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], }), + ('pymatgen', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -- GitLab From 49691e295bac00c8d5dcfa04e643f66f99257cc4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 26 Apr 2017 13:09:36 +0200 Subject: [PATCH 776/818] {lang} [intel/2017a] PyCUDA/2016.1.2 --- ...CUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..102a71dd89 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyCUDA' +version = '2016.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mathema.tician.de/software/pycuda' +description = """PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('CUDA', '8.0.61', '', True), + ('Boost', '1.63.0', versionsuffix), +] + +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ --boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' -- GitLab From ecf4252a307ec2a48fd8b7a0d54a6f2fdfb77605 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 26 Apr 2017 18:29:34 +0200 Subject: [PATCH 777/818] Wrap line --- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb index 102a71dd89..fd93f89fda 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,8 @@ dependencies = [ ('Boost', '1.63.0', versionsuffix), ] -prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ --boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " options = {'modulename': '%(namelower)s'} -- GitLab From 5fc0d21237b193085a426540bd13d4fdd264287c Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 17:00:41 +0200 Subject: [PATCH 778/818] removed built comments --- .../SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 27 +------------------ .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 27 +------------------ 2 files changed, 2 insertions(+), 52 deletions(-) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb index 7d3b72d93e..7e537ec0fb 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -1,9 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-35-15 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## @@ -43,28 +43,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "build_time": 8.34, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a-tools.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1955553, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493148914, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb index 667807f3cc..46e980be5f 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -1,9 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-34-35 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## @@ -37,28 +37,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "build_time": 14.02, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 4336229, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493148875, - "total_memory": 128828, -}] -- GitLab From 898b454611d529f69430652bb58b19dae94a9096 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 17:03:16 +0200 Subject: [PATCH 779/818] removed built comments --- .../easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 27 +---------------- .../i/IMB/IMB-4.1-intel-2017.02.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb index 87a1fa9cc3..0a33899fe9 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-21_09-32-59 easyblock = 'MakeCp' name = 'IMB' @@ -30,28 +29,4 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 17.94, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'IMB-4.1-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1238017, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492759974, - "total_memory": 128828, -}] + diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb new file mode 100644 index 0000000000..65d5fc7e4a --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +toolchain = {'name': 'intel', 'version': '2017.02'} +toolchainopts = {'usempi': True} + +source_urls = ['https://software.intel.com/sites/default/files/managed/34/aa/'] +sources = ['%(name)s_%(version)s.tgz'] + +prebuildopts = "cd src && " +buildopts = "all" + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' + -- GitLab From 0378f98cce404a3d418b2ff997068c303ba29f9d Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:55:18 +0200 Subject: [PATCH 780/818] removed built comments --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 28 +------------------ 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index 7d56604ccc..c2ecdc414e 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -1,10 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-37-09 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer -# License:: 3-clause BSD +## License:: 3-clause BSD # # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ @@ -40,28 +39,3 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 69.0, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'OTF2-2.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 19885165, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493149028, - "total_memory": 128828, -}] -- GitLab From 1763251c00437c70b3aeff0287d6406648f30897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 10:57:26 +0200 Subject: [PATCH 781/818] align IMB 4.1 easyconfigs for foss/2017a and intel/2017.02 --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 14 +++++--------- .../easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb | 11 +++++------ 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb index 0a33899fe9..bcbb961f34 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -4,29 +4,25 @@ name = 'IMB' version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' -description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point -and global communication operations for a range of message sizes. -""" +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" +buildopts = 'all CC="$MPICC"' parallel = 1 files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], 'dirs': ['bin', 'doc'] } moduleclass = 'perf' - - diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb index 65d5fc7e4a..d22113b5a9 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb @@ -10,20 +10,19 @@ description = """The Intel MPI Benchmarks perform a set of MPI performance measu toolchain = {'name': 'intel', 'version': '2017.02'} toolchainopts = {'usempi': True} -source_urls = ['https://software.intel.com/sites/default/files/managed/34/aa/'] sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] -prebuildopts = "cd src && " -buildopts = "all" +start_dir = 'src' +buildopts = 'all CC="$MPICC"' parallel = 1 -files_to_copy = [(['src/IMB-*'], 'bin')] +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], - 'dirs': [], + 'dirs': ['bin', 'doc'] } moduleclass = 'perf' - -- GitLab From 828a4b4be010f44678b5cc7c401ecd2b84ea51d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 11:23:30 +0200 Subject: [PATCH 782/818] adding easyconfigs: Boost-1.64.0-intel-2017a.eb --- .../b/Boost/Boost-1.64.0-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb new file mode 100644 index 0000000000..981136de99 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.64.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From d211df671be83d9fbb2740449366a1874cf44490 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 12:44:47 +0200 Subject: [PATCH 783/818] adding easyconfigs: Python-3.6.1-intel-2017a.eb --- .../p/Python/Python-3.6.1-intel-2017a.eb | 127 ++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb new file mode 100644 index 0000000000..b226f52d51 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -0,0 +1,127 @@ +name = 'Python' +version = '3.6.1' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('XZ', '5.2.3'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' -- GitLab From 6d38e047d7867b3529d97081d4ff1c69857e504c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 14:50:50 +0200 Subject: [PATCH 784/818] adding easyconfigs: BamTools-2.4.1-intel-2017a.eb, CMake-3.8.0-GCCcore-6.3.0.eb --- .../b/BamTools/BamTools-2.4.1-intel-2017a.eb | 16 +++++++++ .../c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb new file mode 100644 index 0000000000..fd92ae4c8f --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'BamTools' +version = '2.4.1' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '3.8.0')] + +files_to_copy = ['bin', 'lib', 'include', 'docs', 'LICENSE', 'README'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..522448447c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9d66b3cd3f23021c0083ce763ee46a4b14b0dbb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:01:10 +0200 Subject: [PATCH 785/818] use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb | 8 ++------ easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb | 8 ++------ easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb | 8 ++------ 3 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 4325e0c729..ad3e944f8a 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'gompi', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] runtest = 'check' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb index 14ebd120a4..2c0fe9cb97 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] # no quad precision, requires GCC v4.6 or higher # see also diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb index da857e5ca5..7d5646bd9c 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] # no quad precision, requires GCC v4.6 or higher # see also -- GitLab From 8a0042c90ca5002241acabd21eae93ec86b751a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:24:03 +0200 Subject: [PATCH 786/818] adding easyconfigs: SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb, SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb, METIS-5.1.0-intel-2017a.eb, ParMETIS-4.0.3-intel-2017a.eb --- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 25 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb | 22 ++++++++++++++++ ...iteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb | 19 ++++++++++++++ ...Sparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb | 19 ++++++++++++++ 4 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb new file mode 100644 index 0000000000..91d00f1139 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -0,0 +1,25 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.8.0')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb new file mode 100644 index 0000000000..239bd0fcd4 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.8.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb new file mode 100644 index 0000000000..3f7ce4f28f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..28aa92c03a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ParMETIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From ab62066363ea6186a345ad2c4c489dc45f355fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:39:36 +0200 Subject: [PATCH 787/818] fix sources spec for HMMER 3.1b2 + minor style fixes --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb | 9 ++++----- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 9 ++++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index 0456b6d6ce..c756d8464e 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -28,16 +28,15 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] -sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], 'dirs': [] } -runtest = 'check' - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index da1af277a5..4211dd88a0 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -28,16 +28,15 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] -sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], 'dirs': [] } -runtest = 'check' - moduleclass = 'bio' -- GitLab From 83ab75f708cba109de54b5c963959c07e8f9b33f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:44:19 +0200 Subject: [PATCH 788/818] extend sanity check for HMMER 3.1b2 --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index c756d8464e..aed3e32ba8 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -35,8 +35,9 @@ runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], - 'dirs': [] + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index 4211dd88a0..66c915507d 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -35,8 +35,9 @@ runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], - 'dirs': [] + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], } moduleclass = 'bio' -- GitLab From 0944579f6e494a7a2e3e626638aa50ea16c951e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:58:00 +0200 Subject: [PATCH 789/818] adding easyconfigs: HMMER-3.1b2-intel-2017a.eb --- .../h/HMMER/HMMER-3.1b2-intel-2017a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb new file mode 100644 index 0000000000..3ca7456fc5 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' -- GitLab From d8b7170e5bdc9bf19490d270f9877692a2e5d9b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:01:29 +0200 Subject: [PATCH 790/818] {compiler}[dummy] GCCcore 7.1.0 --- .../easyconfigs/g/GCCcore/GCCcore-7.1.0.eb | 54 ++++++ .../mpfr-3.1.5-allpatches-20161219.patch | 176 ++++++++++++++++++ 2 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb new file mode 100644 index 0000000000..6f69a58a66 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '7.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.5' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.28'), +] + +patches = [ + ('mpfr-%s-allpatches-20161219.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + 'GCCcore-6.2.0-fix-find-isl.patch', +] + +checksums = [ + '6bf56a2bca9dac9dbbf8e8d1036964a8', # gcc-7.1.0.tar.bz2 + '8ddbb26dc3bd4e2302984debba1406a5', # gmp-6.1.2.tar.bz2 + 'b1d23a55588e3b2a13e3be66bc69fd8d', # mpfr-3.1.5.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch new file mode 100644 index 0000000000..4e70357e4a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -0,0 +1,176 @@ +# MPFR v3.1.5 patch dated 2017-12-19 +# downloaded via https://gforge.inria.fr/frs/?group_id=136 +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; -- GitLab From cf7d72d4c302a22a5ee6946ec7a95f47f1cb9779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:32:15 +0200 Subject: [PATCH 791/818] fix time travelling in MPFR patch, thanks @wpoely86 --- .../easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch index 4e70357e4a..67ff28d57a 100644 --- a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -1,4 +1,4 @@ -# MPFR v3.1.5 patch dated 2017-12-19 +# MPFR v3.1.5 patch dated 2016-12-19 # downloaded via https://gforge.inria.fr/frs/?group_id=136 diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES --- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 -- GitLab From 42e15f650164f4faee57db07337d9dfeabf46332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:36:24 +0200 Subject: [PATCH 792/818] {compiler}[dummy] GCC 7.1.0 w/ binutils 2.28 + deps --- .../b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb | 27 ++++++++++++++++++ .../b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 21 ++++++++++++++ .../f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 24 ++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb | 25 +++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-7.1.0.eb | 24 ++++++++++++++++ .../m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 28 +++++++++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 25 +++++++++++++++++ 7 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..33d3ae47a6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..10ecc14d7a --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..28c855c205 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..870e7eab31 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '7.1.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..f487ba5530 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..18394615f9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..bec9454ed8 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 29988a028e00ce8b88a74b367cd1cfcbd1b4db80 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 3 May 2017 11:22:05 +0200 Subject: [PATCH 793/818] PoC for TBB open source --- .../t/tbb/tbb-2017_U5-goolf-1.7.20.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb new file mode 100644 index 0000000000..94782c17c8 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb @@ -0,0 +1,28 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +unpack_options = '--strip-components=1' + +skipsteps = ['configure', 'install'] + +buildininstalldir = True + +buildopts = "compiler=$CC" + +#runtest = 'compiler=$CC test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['.'], +} + +moduleclass = 'lib' -- GitLab From 60038da4530e4cde6809d03d02b289e8ca841a83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:30:23 +0200 Subject: [PATCH 794/818] also build IMB-IO in IMB 4.1 easyconfig using foss/2016b --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index f6d0b1f028..449a0d2750 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -4,26 +4,24 @@ name = 'IMB' version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' -description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point -and global communication operations for a range of message sizes. -""" +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" +buildopts = 'all CC="$MPICC"' parallel = 1 files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], 'dirs': ['bin', 'doc'] } -- GitLab From 9d83a3a823af6048779169f9eb4272b540b03097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:33:59 +0200 Subject: [PATCH 795/818] adding easyconfigs: IMB-4.1-intel-2017a.eb --- .../easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb new file mode 100644 index 0000000000..6636a983cd --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': ['bin', 'doc'] +} + +moduleclass = 'perf' -- GitLab From 1521762763e6b6414ffd0859c553dc3337f5a038 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:59:21 +0200 Subject: [PATCH 796/818] fix toolchain version --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index 449a0d2750..2b74ec6d38 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes""" -toolchain = {'name': 'foss', 'version': '2016b'} +toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] -- GitLab From a8d022261518aa55ac0044ad7e0b852f1fc55509 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 14:10:11 +0200 Subject: [PATCH 797/818] clean up tbb easyconfig to use enhanced easyblock --- .../easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb index 94782c17c8..f90202e1b4 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb @@ -10,19 +10,4 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/01org/tbb/archive/'] sources = ['%(version)s.tar.gz'] -unpack_options = '--strip-components=1' - -skipsteps = ['configure', 'install'] - -buildininstalldir = True - -buildopts = "compiler=$CC" - -#runtest = 'compiler=$CC test' - -sanity_check_paths = { - 'files': [], - 'dirs': ['.'], -} - moduleclass = 'lib' -- GitLab From b2623eb814ff0c54f95850202907564ac4768734 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 14:20:28 +0200 Subject: [PATCH 798/818] adding easyconfigs: tbb-2017_U5-intel-2017a.eb --- .../easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb new file mode 100644 index 0000000000..fc7398b13b --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb @@ -0,0 +1,13 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +moduleclass = 'lib' -- GitLab From 775f59f8c5345bb4ddb974790de0275d68e88e29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 16:47:33 +0200 Subject: [PATCH 799/818] adding easyconfigs: Node-RED-0.16.2-foss-2017a.eb, nodejs-6.10.3-foss-2017a.eb --- .../n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 28 +++++++++++++++++++ .../n/nodejs/nodejs-6.10.3-foss-2017a.eb | 26 +++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb new file mode 100644 index 0000000000..828c4e612b --- /dev/null +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'Node-RED' +version = '0.16.2' + +homepage = 'http://nodered.org' +description = """Node-RED is a programming tool for wiring together hardware devices, APIs and online services + in new and interesting ways.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/node-red/node-red/releases/download/%(version)s/'] +sources = ['node-red-%(version)s.zip'] + +dependencies = [ + ('nodejs', '6.10.3'), +] + +preinstallopts = 'cd %(namelower)s-%(version)s && ' +install_cmd = 'npm install --prefix %(installdir)s -g' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/node_modules/%(namelower)s'], +} +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb new file mode 100644 index 0000000000..65377857a3 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '6.10.3' + +homepage = 'http://nodejs.org' + +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'lowopt': True} + +source_urls = ['http://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' -- GitLab From 012625a422c61cf81f51b20892b4413d2891039f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 17:20:32 +0200 Subject: [PATCH 800/818] more %(namelower)s --- easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb index 828c4e612b..7531db7616 100644 --- a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -10,7 +10,7 @@ description = """Node-RED is a programming tool for wiring together hardware dev toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['https://github.com/node-red/node-red/releases/download/%(version)s/'] -sources = ['node-red-%(version)s.zip'] +sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ ('nodejs', '6.10.3'), -- GitLab From f9589ba77bc83a6b6e568a99c9de6b0958733f10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 17:27:30 +0200 Subject: [PATCH 801/818] use --help as sanity check command, since --version starts a Node-RED server... --- easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb index 7531db7616..f11db814aa 100644 --- a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -23,6 +23,6 @@ sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['lib/node_modules/%(namelower)s'], } -sanity_check_commands = ['%(namelower)s --version'] +sanity_check_commands = ['%(namelower)s --help'] moduleclass = 'tools' -- GitLab From a3a0e6c3c840bbd9e2ac747879d5fb04bceb7223 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 May 2017 12:21:44 +0800 Subject: [PATCH 802/818] prepare release notes for eb320 --- RELEASE_NOTES | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a56c5c3afe..b25f9e1c1c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,32 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.2.0 (May 5th 2017) +--------------------- + +feature release +- added example easyconfig files for 33 new software packages: + - ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484), + DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450), + imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), PyCUDA (#4523), + pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), + SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), + VMD (#4391), WRF-Fire (#4403) +- added additional easyconfigs for various supported software packages, including ... +- various enhancements, including: + - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) + - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) +- various bug fixes, including: + - add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369) + - use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384) + - fix pkgconfig patch for Qhull to only let CMake substitute (#4451) + - also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467) + - add dependency NLopt for R extension nloptr (#4481) + - fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504) + - change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505) + - fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531) + + v3.1.2 (March 20th 2017) ------------------------ -- GitLab From 23d840436deca449424710bd1abe199149a27d7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 May 2017 13:50:49 +0800 Subject: [PATCH 803/818] prepare release notes for eb320 --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b25f9e1c1c..f2fbd7d51c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -17,7 +17,8 @@ feature release pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), VMD (#4391), WRF-Fire (#4403) -- added additional easyconfigs for various supported software packages, including ... +- added additional easyconfigs for various supported software packages, including: + - 3to2 1.1.1, ACTC 1.1, ALLPATHS-LG 52488, Autoconf 2.69, Autoconf 2.69, Automake 1.15, Automake 1.15, Autotools 20150215, Autotools 20150215, arpack-ng 3.4.0, atomate 0.4.4, BLAT 3.5, BamTools 2.4.1, BioKanga 4.3.4, BioKanga 4.3.5, BioPerl 1.7.1, Bison 3.0.4, Boost 1.63.0, Boost 1.64.0, Bowtie2 2.2.9, BreakDancer 1.4.5, binutils 2.28, bx-python , bzip2 1.0.6, CMake 3.8.0, CUDA 8.0.61.eb, Cantera 2.3.0, ClusterShell 1.7.3.eb, cURL 7.53.1, cURL 7.54.0, cairo 1.14.8, configparser 3.5.0, cuDNN 6.0, custodian 1.1.0, DBG2OLC 20170208, DFTB+ 1.3.1, Doris 4.02, Doxygen 1.8.13, deap 0.9.2, ED2 20170201, ED2 20170201, ESMF 6.3.0rp1, EasyBuild 3.1.2.eb, Eigen 3.3.2, entrypoints 0.2.2, FFTW 3.3.6, FireWorks 1.4.2, file 5.30, flex 2.6.3, fmt 3.0.1, fontconfig 2.12.1, fqtrim 0.9.5, freetype 2.5.5, freetype 2.6.2, freetype 2.7.1, freetype 2.7.1, GCC 6.3.0, GCC 7.1.0, GCCcore 7.1.0.eb, GDAL 2.1.3, GEOS 3.6.1, GETORB 2.3.2, GLib 2.52.0, GMP 6.1.2, GSL 2.3, GapFiller 2.1.1, Ghostscript 9.21, Go 1.8.1.eb, g2clib 1.6.0, g2lib 1.4.0, gnuplot 5.0.5, googletest 1.8.0, HDF 4.2.12, HDF5 1.10.0, HISAT2 2.0.5, HMMER 3.1b2, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, hwloc 1.11.6, IMB 4.1, IMB 4.1, IMB 4.1, IPy 0.83.eb, IPython 5.3.0, ImageMagick 7.0.5, Inspector 2017_update2.eb, imbalanced-learn 0.2.1, ipyrad 0.6.15, JasPer 1.900.1, JasPer 2.0.12, jemalloc 4.5.0, LIBSVM 3.22, LLVM 4.0.0, LZO 2.10, LibTIFF 4.0.7, LittleCMS 2.8, libGLU 9.0.0, libdrm 2.4.76, libiconv 1.15, libjpeg-turbo 1.5.1, libpng 1.6.18, libpng 1.6.21, libpng 1.6.28, libpng 1.6.29, libreadline 7.0, libsodium 1.0.12, libtool 2.4.6, libtool 2.4.6, libxml2 2.9.4, libyaml 0.1.7.eb, M4 1.4.18, METIS 5.1.0, MRtrix 0.3.15, Mako 1.0.6, Mesa 17.0.2, MultiQC 0.7, MultiQC 0.9, makedepend 1.0.5, matplotlib 1.5.1, matplotlib 2.0.0, matplotlib 2.0.0, NASM 2.12.02, NGS 1.3.0, NLopt 2.4.2, NLopt 2.4.2, ncbi-vdb 2.8.2, ncurses 6.0, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, netCDF 4.4.1.1, nettle 3.3, numba 0.32.0, numpy 1.10.1, numpy 1.12.1, ORCA 4.0.0.2, Octave 4.2.1, OpenMPI 2.1.0, OpenPGM 5.2.122, PCRE 8.40, PETSc 3.7.5, PGI 17.3, PLINK 1.9b_4.1, PROJ 4.9.3, ParMETIS 4.0.3, Perl 5.24.1, Pillow 4.1.0, PyCUDA 2016.1.2, PyYAML 3.12, PyYAML 3.12.eb, PyZMQ 16.0.2, Python 2.7.13, Python 3.6.1, pixman 0.34.0, pkg-config 0.29.2, pkgconfig 1.2.2, pymatgen-db 0.6.5, pymatgen 4.7.3, QuTiP 4.1.0, QuantumESPRESSO 6.1, R 3.3.3, R 3.3.3, ROI_PAC 3.0.1, Rascaf 1.0.2, RepastHPC 2.2.0, rootpy 0.8.0, SAMtools 0.1.20, SAMtools 1.4, SAMtools 1.4, SCons 2.5.1, SIONlib 1.7.1, SIONlib 1.7.1, SQLite 3.17.0, SSPACE_Basic 2.1.1, SUNDIALS 2.7.0, SWASH 3.14, SWASH 3.14, SWIG 3.0.12, Sambamba 0.6.6.eb, Seaborn 0.7.1, Spack 0.10.0.eb, SpiceyPy 1.1.0, StaMPS 3.3b1, Stacks 1.45, Stacks 1.46, Stampy 1.0.31, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, samblaster 0.1.24, scipy 0.19.0, scp 0.10.2, snaphu 1.4.2, sparsehash 2.0.3, spglib-python 1.9.9.38, Tcl 8.6.6, Tk 8.6.6, Triangle 1.6, tbb 2017_U5, tbb 2017_U5, tcsh 6.20.00, UDUNITS 2.2.24, util linux, VMD 1.9.3, VTune 2017_update2.eb, ViennaRNA 2.3.5, vsc-base 2.5.8, vsc-install 0.10.25, vsc-mympirun 4.0.0b0, WRF-Fire 20170221, WRF 3.8.0, Wannier90 2.1.0, X11 20170314, XZ 5.2.2, xorg-macros 1.19.1, xproto 7.0.31, ZeroMQ 4.2.2, zlib 1.2.11, zlib 1.2.11 - various enhancements, including: - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) -- GitLab From 64164034dc03ed67cc9cf24fef855d8a71878eb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2017 09:35:28 +0200 Subject: [PATCH 804/818] add comment on Python as build dep for nodejs --- easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb index 65377857a3..b02123940f 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -16,6 +16,7 @@ toolchainopts = {'lowopt': True} source_urls = ['http://nodejs.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] +# Python is required (only) as build dependency allow_system_deps = [('Python', SYS_PYTHON_VERSION)] sanity_check_paths = { -- GitLab From c673a9aa8a3d703806f3201b950947d051eba7c5 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 4 May 2017 15:51:53 +0200 Subject: [PATCH 805/818] adding easyconfigs: git-2.12.2-foss-2016b.eb --- .../g/git/git-2.12.2-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb b/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb new file mode 100644 index 0000000000..4708565849 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.12.2' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.49.1'), + ('expat', '2.2.0'), + ('gettext', '0.19.8'), + ('Perl', '5.24.0', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 26710fc9b17f4bbed3ad2f9de260e16ca650da40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2017 22:34:40 +0200 Subject: [PATCH 806/818] bump version to 3.2.0 + tweak release notes --- RELEASE_NOTES | 18 ++++++++++-------- setup.py | 2 +- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f2fbd7d51c..d67162b731 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,34 +3,36 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, +The latest version of easybuild-easyconfig provides 6,943 easyconfig files, for 1,216 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.2.0 (May 5th 2017) --------------------- feature release -- added example easyconfig files for 33 new software packages: +- added example easyconfig files for 34 new software packages: - ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484), DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450), - imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), PyCUDA (#4523), - pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), - SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), - VMD (#4391), WRF-Fire (#4403) + imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), Node-RED (#4542), + PyCUDA (#4523), pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), + rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), + samblaster (#4435), VMD (#4391), WRF-Fire (#4403) - added additional easyconfigs for various supported software packages, including: - - 3to2 1.1.1, ACTC 1.1, ALLPATHS-LG 52488, Autoconf 2.69, Autoconf 2.69, Automake 1.15, Automake 1.15, Autotools 20150215, Autotools 20150215, arpack-ng 3.4.0, atomate 0.4.4, BLAT 3.5, BamTools 2.4.1, BioKanga 4.3.4, BioKanga 4.3.5, BioPerl 1.7.1, Bison 3.0.4, Boost 1.63.0, Boost 1.64.0, Bowtie2 2.2.9, BreakDancer 1.4.5, binutils 2.28, bx-python , bzip2 1.0.6, CMake 3.8.0, CUDA 8.0.61.eb, Cantera 2.3.0, ClusterShell 1.7.3.eb, cURL 7.53.1, cURL 7.54.0, cairo 1.14.8, configparser 3.5.0, cuDNN 6.0, custodian 1.1.0, DBG2OLC 20170208, DFTB+ 1.3.1, Doris 4.02, Doxygen 1.8.13, deap 0.9.2, ED2 20170201, ED2 20170201, ESMF 6.3.0rp1, EasyBuild 3.1.2.eb, Eigen 3.3.2, entrypoints 0.2.2, FFTW 3.3.6, FireWorks 1.4.2, file 5.30, flex 2.6.3, fmt 3.0.1, fontconfig 2.12.1, fqtrim 0.9.5, freetype 2.5.5, freetype 2.6.2, freetype 2.7.1, freetype 2.7.1, GCC 6.3.0, GCC 7.1.0, GCCcore 7.1.0.eb, GDAL 2.1.3, GEOS 3.6.1, GETORB 2.3.2, GLib 2.52.0, GMP 6.1.2, GSL 2.3, GapFiller 2.1.1, Ghostscript 9.21, Go 1.8.1.eb, g2clib 1.6.0, g2lib 1.4.0, gnuplot 5.0.5, googletest 1.8.0, HDF 4.2.12, HDF5 1.10.0, HISAT2 2.0.5, HMMER 3.1b2, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, hwloc 1.11.6, IMB 4.1, IMB 4.1, IMB 4.1, IPy 0.83.eb, IPython 5.3.0, ImageMagick 7.0.5, Inspector 2017_update2.eb, imbalanced-learn 0.2.1, ipyrad 0.6.15, JasPer 1.900.1, JasPer 2.0.12, jemalloc 4.5.0, LIBSVM 3.22, LLVM 4.0.0, LZO 2.10, LibTIFF 4.0.7, LittleCMS 2.8, libGLU 9.0.0, libdrm 2.4.76, libiconv 1.15, libjpeg-turbo 1.5.1, libpng 1.6.18, libpng 1.6.21, libpng 1.6.28, libpng 1.6.29, libreadline 7.0, libsodium 1.0.12, libtool 2.4.6, libtool 2.4.6, libxml2 2.9.4, libyaml 0.1.7.eb, M4 1.4.18, METIS 5.1.0, MRtrix 0.3.15, Mako 1.0.6, Mesa 17.0.2, MultiQC 0.7, MultiQC 0.9, makedepend 1.0.5, matplotlib 1.5.1, matplotlib 2.0.0, matplotlib 2.0.0, NASM 2.12.02, NGS 1.3.0, NLopt 2.4.2, NLopt 2.4.2, ncbi-vdb 2.8.2, ncurses 6.0, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, netCDF 4.4.1.1, nettle 3.3, numba 0.32.0, numpy 1.10.1, numpy 1.12.1, ORCA 4.0.0.2, Octave 4.2.1, OpenMPI 2.1.0, OpenPGM 5.2.122, PCRE 8.40, PETSc 3.7.5, PGI 17.3, PLINK 1.9b_4.1, PROJ 4.9.3, ParMETIS 4.0.3, Perl 5.24.1, Pillow 4.1.0, PyCUDA 2016.1.2, PyYAML 3.12, PyYAML 3.12.eb, PyZMQ 16.0.2, Python 2.7.13, Python 3.6.1, pixman 0.34.0, pkg-config 0.29.2, pkgconfig 1.2.2, pymatgen-db 0.6.5, pymatgen 4.7.3, QuTiP 4.1.0, QuantumESPRESSO 6.1, R 3.3.3, R 3.3.3, ROI_PAC 3.0.1, Rascaf 1.0.2, RepastHPC 2.2.0, rootpy 0.8.0, SAMtools 0.1.20, SAMtools 1.4, SAMtools 1.4, SCons 2.5.1, SIONlib 1.7.1, SIONlib 1.7.1, SQLite 3.17.0, SSPACE_Basic 2.1.1, SUNDIALS 2.7.0, SWASH 3.14, SWASH 3.14, SWIG 3.0.12, Sambamba 0.6.6.eb, Seaborn 0.7.1, Spack 0.10.0.eb, SpiceyPy 1.1.0, StaMPS 3.3b1, Stacks 1.45, Stacks 1.46, Stampy 1.0.31, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, samblaster 0.1.24, scipy 0.19.0, scp 0.10.2, snaphu 1.4.2, sparsehash 2.0.3, spglib-python 1.9.9.38, Tcl 8.6.6, Tk 8.6.6, Triangle 1.6, tbb 2017_U5, tbb 2017_U5, tcsh 6.20.00, UDUNITS 2.2.24, util linux, VMD 1.9.3, VTune 2017_update2.eb, ViennaRNA 2.3.5, vsc-base 2.5.8, vsc-install 0.10.25, vsc-mympirun 4.0.0b0, WRF-Fire 20170221, WRF 3.8.0, Wannier90 2.1.0, X11 20170314, XZ 5.2.2, xorg-macros 1.19.1, xproto 7.0.31, ZeroMQ 4.2.2, zlib 1.2.11, zlib 1.2.11 + - BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0, + PETSc 3.7.5, PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5 - various enhancements, including: - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) - various bug fixes, including: - add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369) - use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384) - - fix pkgconfig patch for Qhull to only let CMake substitute (#4451) + - fix pkgconfig patch for Qhull (#4451) - also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467) - add dependency NLopt for R extension nloptr (#4481) - fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504) - change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505) - fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531) + - also build IMB-IO in IMB 4.1 easyconfig using foss/2016a (#4539) v3.1.2 (March 20th 2017) diff --git a/setup.py b/setup.py index 0683e432c9..40e8813698 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.0.dev0' +VERSION = '3.2.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 79ac6ae1634c2272cc3f821d2f56ee53ee6d67ee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:10:45 +0200 Subject: [PATCH 807/818] Bump all to CMake 3.8.0 --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../c/CMake/CMake-3.7.2-intel-2017a.eb | 31 ------------------- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 2 +- .../ParaView-5.2.0-intel-2017a-mpi.eb | 2 +- 4 files changed, 3 insertions(+), 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index da60ff72f0..e83b067d66 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -23,7 +23,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.7.2'), + ('CMake', '3.8.0'), ('Eigen', '3.3.3'), ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb deleted file mode 100644 index d78b6b43f1..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.7.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2j'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb index 352a974db9..91d00f1139 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -18,7 +18,7 @@ source_urls = [ # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] -builddependencies = [('CMake', '3.7.2')] +builddependencies = [('CMake', '3.8.0')] configopts = ['', 'shared=1'] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index 903174f12f..8746599786 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -24,7 +24,7 @@ dependencies = [ ('Python', '2.7.13'), ] -builddependencies = [('CMake', '3.7.2')] +builddependencies = [('CMake', '3.8.0')] separate_build_dir = True -- GitLab From 946baf954570a740f5d87d4161d1d75b0bf27b3d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:11:55 +0200 Subject: [PATCH 808/818] Bump CMake in OpenFOAM too to 3.8.0 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index 2469f2947a..c3f3f806f9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [ ('Bison', '3.0.4'), - ('CMake', '3.7.2'), + ('CMake', '3.8.0'), ('flex', '2.6.3'), ] -- GitLab From fcc2fe709d80ba7fe6a6a2d350398621c54022c7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:19:50 +0200 Subject: [PATCH 809/818] Drop old comment --- easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb index fc41f1c1fd..ab4ae0dab8 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb @@ -26,7 +26,7 @@ configopts = '-skip qtgamepad' dependencies = [ ('GLib', '2.52.0'), ('libpng', '1.6.29'), - ('X11', '20170314'), #, '', ('GCCcore', '6.3.0')), + ('X11', '20170314'), ('libGLU', '9.0.0'), ] -- GitLab From 94fab13de92516a969d7a43238c3571870007b1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 May 2017 17:29:28 +0200 Subject: [PATCH 810/818] adding easyconfigs: EasyBuild-3.2.0.eb --- .../e/EasyBuild/EasyBuild-3.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb new file mode 100644 index 0000000000..d84e16eaba --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.2.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/2c/39/4435097a0b897ca1e3c7f055000ebfa2a5dc3632e606a7cf0088b0caa2ee/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/ce/49/70a1d3f419ffb21dc3a3446bdf63d2a49447753fa4e69ec0a3db5a262e67/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/97/59/b8d166b270f113ae69b0983275dac5da5bfb94bb1082a10bb26e93c78ed7/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From b1d56530a5bae608a28c907a43792ed3c9f85ea6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 May 2017 17:58:30 +0200 Subject: [PATCH 811/818] bump to v3.3.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 40e8813698..85590c2983 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.0' +VERSION = '3.3.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 2a8958f86f854c0523d195c3bf3a34edb6615ef6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:26:00 +0200 Subject: [PATCH 812/818] adding easyconfigs: OpenFOAM-2.2.2-intel-2017a.eb, flex-2.5.39-GCCcore-6.3.0.eb --- .../f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 22 +++++++++++ .../o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb | 39 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f579ff8a96 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -0,0 +1,22 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.18')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb new file mode 100644 index 0000000000..7d4fcb2a52 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' +version = '2.2.2' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.2.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From 0fee12a842bff40dfac37d47d96db9e9137ffb2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:28:24 +0200 Subject: [PATCH 813/818] adding easyconfigs: OpenFOAM-2.3.1-intel-2017a.eb --- .../o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb new file mode 100644 index 0000000000..22826bc9df --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb @@ -0,0 +1,44 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From d3563b795447df65ba2eaaf239c0f332589a3c50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:29:03 +0200 Subject: [PATCH 814/818] adding easyconfigs: OpenFOAM-2.4.0-intel-2017a.eb --- .../o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb new file mode 100644 index 0000000000..dd2ccbb6b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From 8d7635554191701bb4b415e9a5fce845e981f221 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 May 2017 09:52:09 +0200 Subject: [PATCH 815/818] adding easyconfigs: ASE-3.13.0-intel-2017a-Python-2.7.13.eb --- .../ASE-3.13.0-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..046d2d02c9 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From d3dd9379507508f02b36714605f0a22ae9bc187d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 May 2017 10:16:35 +0200 Subject: [PATCH 816/818] adding easyconfigs: hanythingondemand-3.2.2-cli.eb, hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb --- .../hanythingondemand-3.2.2-cli.eb | 42 +++++++++++++++++++ ...ndemand-3.2.2-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb new file mode 100644 index 0000000000..5c43bd66c7 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.2' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.8'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # specify location on shared 'scratch' filesystem for HOD working directories + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ef65fdbca6 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.12'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' -- GitLab From c22ad8a61d53d5c2f32a5f02e6744227475d3416 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 09:46:50 +0200 Subject: [PATCH 817/818] don't re-add archived libpciaccess easyconfigs --- .../libpciaccess-0.13.1-ictce-4.0.6.eb | 24 ------------------- .../libpciaccess-0.13.1-ictce-4.1.13.eb | 24 ------------------- 2 files changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb deleted file mode 100644 index adbb940942..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -builddependencies = [ - ('Autoconf', '2.69'), - ('xorg-macros', '1.17'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb deleted file mode 100644 index 67891759ae..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -builddependencies = [ - ('Autoconf', '2.69'), - ('xorg-macros', '1.17'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' -- GitLab From 44b396a0cef6d3a4c19f55157e03ab3932b184bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 09:48:20 +0200 Subject: [PATCH 818/818] consistent update of libpciaccess source URLs --- .../l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 4 +--- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb | 4 +--- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 01c9c7b5d7..9967c64c68 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'GCC', 'version': '4.7.2'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb index 11ed8ea67d..76bd735f5a 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'foss', 'version': '2016b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb index 9124b553ab..de4d55b188 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab