diff --git a/.travis.yml b/.travis.yml index 13ca5c06124cde891f9985517b0315b7d63358b2..07cebed7383024955eb896106fc2913f24c05718 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 diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 3ed16807e4006b18697ed57048bffc9ea2391d5b..d67162b731a6526bdb8591cc99298c1f98ee5361 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,134 @@ 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 6,943 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 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), 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: + - 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 (#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) +------------------------ + +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, #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) +- various bug fixes, including: + - correctly set $PYTHONPATH in ROOT easyconfigs (#4239, #4331) + - correct libjpeg turbo references in GDAL (#4276) + - make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (#4278) + - fix issues with miRDeep2 installation (#4291, #4301, #4316) + - also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - fix PostgreSQL homepage + minor style fixes (#4318) + - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) + - 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) +----------------------- + +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), + Smoldyn (#4110), SpiecEasi (#4215), stress (#4180) +- added additional easyconfigs for various supported software packages, including: + - 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: + - 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: + - add Bison and gettext as build deps for X11 (#4111) + - 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 (#4133, #4164, #4177) + - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) + - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) + - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) + - 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) + - 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) +-------------------------- + +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), + 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) + - 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) + - 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 + 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/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 0000000000000000000000000000000000000000..5236c8830ea73e3274f68faf1ee2d7da33dac2f4 --- /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' 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 094f64851263b26e234b3e09ce596b69f1f96f8c..1b2933e3cadc68120c13a8dab4d391c66418fda0 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 f899ce8f01ef0aa926aa3c5c19d2286a14c7a788..e7d7f8108ea8f83aa357d5d54ccaaec4c8de1754 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 2063066a889925d36cd7747413d2c49899664c6e..77fcbc5c082d524a56a9f56dc70e626dfb1fc914 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/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..47b6a5d46fbb4853497a2f9ab51640e70b20a31a --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +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] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +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', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/ac'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb index 045e5244fde9823bc6ae0d11047ac403fa5285d2..f7098831f652999e23a7b4c55be6aa40ba1378e8 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 21843552e81463d6e6cf4449756188b70c9811c4..a094b11d6d9f83353c4df10897628894c5a4b992 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 5fe5e14c146083d6f013deb7017b3af4199b8707..6c3aae43602b3e46391eae2e527e552b1b563756 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/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 bde2863301918dcf07cd88c34edf095a1dbcca8a..6fb42921f6b33fdea0a5dd694689d564e5aee6ef 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/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 0000000000000000000000000000000000000000..0227efebd7e0c85b6fcea15f72a1f01e73184588 --- /dev/null +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -0,0 +1,36 @@ +## +# 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.""" + +# Compilation fails with GCC 5.3 (foss-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', +] +sources = ['allpathslg-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..4c41ac6ecec933a60113742b3c19c63a48ef7318 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'ALPS' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://alps.comp-phys.org/" +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'} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases/'] + +dependencies = [ + ('CMake', '3.6.2'), + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('HDF5', '1.8.17') +] + +separate_build_dir = True + +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 new file mode 100644 index 0000000000000000000000000000000000000000..3d3e67389f1cf94396b3440844c39a452010b9d6 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'ALPS' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://alps.comp-phys.org/" +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'} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases/'] + +dependencies = [ + ('CMake', '3.6.2'), + ('Python', '3.5.2'), + ('Boost', '1.63.0', versionsuffix), + ('HDF5', '1.8.17') +] + +separate_build_dir = True + +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/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index 1e7fda13a16fd9fbb8e218c3ea48b5c3b2a98cc2..a251f6e6b49696865871a175264b70f8293420ef 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' @@ -12,18 +12,18 @@ 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"] +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/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 0000000000000000000000000000000000000000..357880d1409cceb32239c4af9f106b558146c623 --- /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/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 0e9c615ba9e4688d23e225e1a57f772b20998545..70205ebf3a4276d87179e2495dffdae4211da653 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 22d5bebaad96415f872801708a48f949f4213876..6e2edca0dc6332b5bbd3e68cb0a687ec2cd1bf90 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/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 9a71b607bea2787595926570ae7ddc408b9a3dd3..5f9521e1fef7fef63d62f50e96b3527b1f0f0e1d 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/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 4e451954c3f1494e862623f8d2135b3e5dcf8c38..4e75833d6eab8e595ca28fb7a24234ea6a49fc38 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 f910ba5400d6490aaea890df7a1c04778556fc3e..b2fcc5fadab861c8da9c173427bf41afbadebe83 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 1b29f57d52d51cbed31bce2236f58f3d5e8f7f9d..8895c479d830921b4729ab517d2f59ed32e55cad 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/Anaconda2/Anaconda2-4.2.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..3fe1b814e4e6712a7622c7f60845f5aded1c500b --- /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 0000000000000000000000000000000000000000..9d27c79985c067e2bc6c98f6dfceee5472d520ec --- /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' 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 0000000000000000000000000000000000000000..8f548fef7deec7721942f01c1ce58d6d70ba845e --- /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/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 0000000000000000000000000000000000000000..509aa4c19abc836d627d9862f1b2fa7a56114145 --- /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' 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 3d86e53a57f037ea9931834a3707ac8ddb324b5c..552c3eb907b506d28f28d59bba3b64009bf46bb3 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-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..765fe6f2fd3e40f3023891635ddb2cc4094d3c93 --- /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/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 0000000000000000000000000000000000000000..84aebc0f8fc41b5bce9cddf73f60e80b67253e1f --- /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/Autoconf/Autoconf-2.69-foss-2015b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..408f488ecafacbe48cf1af1579ea3b0e42b5ad6c --- /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/Autoconf/Autoconf-2.69-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb index 1e344106ca7e9ec2001ba363e44c34dbe9336a19..612bf18994c3fdb1c2982148335381ed9ae7b5a9 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/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 0000000000000000000000000000000000000000..0d4c530534c52d8d3bd1f8713f5b9778c770757e --- /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/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 0000000000000000000000000000000000000000..304170650f6431854ebbb0331e1940a519a5bfe4 --- /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/Automake/Automake-1.15-foss-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..543e7a0ba7cabf0b31c17c77bb2b2591f630198a --- /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' 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 0000000000000000000000000000000000000000..79f6723eb65fbbc4edb6dd8c9bcff68d61eff069 --- /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/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 0000000000000000000000000000000000000000..9e2d66a8e21b07e9f6c29790191726fe3f16f7c1 --- /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/a/Autotools/Autotools-20150215-foss-2015b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab4ec5f14918b96040ec1cc1b6d14492b9628131 --- /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' 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 c9d9db6e85f23d4f549a6c88f5345ccf584ee1b9..39352e91cb8b2e932e963897ae73a9f231af30ae 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/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 0000000000000000000000000000000000000000..d2ebd371892f6bca3f5794111f3e5d3851bc705b --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -0,0 +1,26 @@ +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/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 0000000000000000000000000000000000000000..42ed3e6196649276479ff9aca920896c5065813c --- /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/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 69f6af4aa8fb4fbe0ec615f5448a8cbd59a29875..ffe0aa3aaf40ea5685a930ec05a28b4ca0c80359 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 ed48c6519163f1477087294f08a5f29eef26ac8c..f37d535fe6b22a630edeff6d52ec7631eaa98719 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 4e4944c69eefc7a331c467bfea5d31d1c4eda25f..7a79bafbc3fac66cda3939ee1938abdb8257f6d5 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 b01a6297fc1fbbc82b93bb6c65bd38c2b2bddd59..ab777254e94e2f21453235b516972d7b4c1dff43 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 ad986bd5761fcf97181c6da1d76c2b481707d0e8..03ba48168e709f8df658eb665c8ea54807dbd3ae 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 e1662e8bf27e897b781f6ba669d0f911701f672f..986e3e5a6f6b34ce39fcf5647b107064f9e2f9b7 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 7da7aa32db660ca1155cce7adcd65c6eeabaf168..6036bb0be83b2b9f80338ae49c06de71e86f2301 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 3ee7c5b406ade6929d3a8426c37ec64041e5e8df..d51a118fba3ea5fcf6f5f1c18f68aec7bd0fca2a 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 d93ecdb14ed240d4746ce39b63527dfa86ffc607..0e7df6fdf18876d2e12405cb15a5aa29850c39aa 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 b048fcd09766b3fd62f1405afc3618e15e3a6eb1..33aa30131b0c4f869109703b237b0ea0621c6508 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 407fa7e1c06d7edf8e51d6edb1b96f91ca75fe71..0f10c1689bcd786e8850c63a4e1a549abe59ff88 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 08bcaf86cf6b0470f2a4cd82464073fd0ca4b974..f22f0e01b793541ac49460e3aecaf55b61471f3f 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': ''} 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 186bcfb543dfa7b7ca1455aa97a55cd4878f7929..4c6e292088e22f88b0a2d04483a27e7bc47a2aba 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 @@ -1,10 +1,11 @@ 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 - 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/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 38638c65fbf0f9a711c4c2b3d74e072d5c5b03ab..4562fea8de15219907d742c23f8615d79451d53d 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 +10,10 @@ 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'] + +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] # 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 e567606aa794550bbccde08549e14c3cd0bb6930..36abbfba392a2f9a4748090aa5cd087060455104 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 +9,10 @@ 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'] + +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] # 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 837fa583de8227269041736e851dabc8dca952a8..a63af2d1973d5248dd3e13c346eea6be0f1ee4cf 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 +10,10 @@ 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'] + +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] # 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 15e7a3b7340f8e24a785922f841b0b747b75e797..e390bd7768492ef1c75ce261898f4a96c66e4049 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 +9,10 @@ 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'] + +checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] # 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 6388557ca2e36779a47b074157e8af97eb23f664..b22908df9d3b42cbe74b5b8e46e692753b2f40e8 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 +10,10 @@ 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'] + +checksums = ['d84e1b6108d9ee67c0d21aba7099e953'] 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 15bec194bef84d4784df2567b0df9191892d0834..cdb3eae35c1e057ca91f491d9ed41b3537d4ff12 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 +9,10 @@ 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'] + +checksums = ['d84e1b6108d9ee67c0d21aba7099e953'] configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' 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 0000000000000000000000000000000000000000..9320f188ec08fcfc6f4974c34b44af62e8694f6b --- /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' 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 0000000000000000000000000000000000000000..f7c3095a503848ebfcd3e33701e3b9e59636ab29 --- /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.%s" % SHLIB_EXT], + '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 0000000000000000000000000000000000000000..17c7254907cda2a5a892484e15e8f833508e57a4 --- /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.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' 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 0000000000000000000000000000000000000000..6a33cf7fb22b9258b8b59a4a54540e6fe4013c6e --- /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/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 0000000000000000000000000000000000000000..729a10008fffa03070862c564fd8d5809053da36 --- /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' 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 cd21d99d6dc351766a83e5d327afc2b04a1fcd5d..938cb4bc7e4b3213b04d9d7a664722630df1eb58 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' @@ -30,7 +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.""" +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 dff5ba78e2147f145ff3dbd825d9c76cafac3dfc..83c91ab617bf48136d5ed0f4ceefa4ecb58f3dbe 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' @@ -30,7 +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.""" +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 539e3c2d208966150d41c119bd2662d4d21d03b9..52eabb1bfe2483b45ea6dde46de5d343863fee2e 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)] @@ -28,7 +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.""" +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/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 2ee4f6221607759d9e9abc625910ca00fc599073..3ef62f1ae2bc2fc8f074a7966e5d8c0c89b930f8 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 f9319eca14c9ad0a98ecc06c96987eb6eeca51fd..41baab6d42d9b436071459a6f1738d04d7fec080 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 6d469bdd3bfdf8170b2cbb1329fd00c1b6e73eda..a0b589e82c4cd85044fa94b32e246fbbf514a468 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 bd1b04228ad5d8688b0adb35bfa1817fcad47f32..af2dc1fef753e8f22ba4c5a624d4aca0e7656c27 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 47aaf73fa3241d5c495936f0d30d078e055ac2a6..4ed43caefda734f67b79ac512707706e25394aeb 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/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 7b47764f4758e9a58c3799462d24c2eb6e6f480b..1461dc4f22af0143df965c22b7620739e55fcfed 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 new file mode 100644 index 0000000000000000000000000000000000000000..d31c4ec289a464ada095476ffba9f9e062edfe4e --- /dev/null +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -0,0 +1,40 @@ +# 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'] + +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= ' + +installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/blasr"], + 'dirs': [], +} + +moduleclass = 'bio' 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 afbf2938b8da643d2de1f4b9e58480c0d56f8082..eb88b061dde0914f10ed131170fa05bf723873fa 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 e2d58bafb6395314a0d65cc6a303f5f045a39735..0222da154644c5563efe5738eb78b4f5defbd065 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 5f6044dcecc24f8ff7342009412311871a64b60f..955ee61e307871f150786bba41b4efd4539755bc 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/BLAT/BLAT-3.5-intel-2016b.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..48a47daaa1124160db1915c3c331695f3efbecde --- /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' 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 0000000000000000000000000000000000000000..7e57ded0421cbd6eb4919f5c12e00295b9393cff --- /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' 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 9cbb01f19159fdaa5eb5f8bfa09132d8eab17325..2dbdeeb980092decdf7fa4ca064efc1f23dad61a 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 9cd875e7c60fa38c6eb4476b15a970310707c439..c0802f9dddb138b7168814c3ab3a0c8c7b06bd89 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/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 0000000000000000000000000000000000000000..d0e6af59d8a66eb8fba0e39345d991f1d411e9fc --- /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' 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 0000000000000000000000000000000000000000..fd92ae4c8fca64f8f2703031d489985699f32673 --- /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/b/BayPass/BayPass-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb index e948c06e11a279562b5b09a1b6b78bb55c0e28aa..65f14b74d86062815839d359385220793ead7603 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/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb index cd1dd2595af31e41000bba732fd8b4053ec560ec..25707a1810d10bf021087a30bf63a21a2e233e2a 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 7a976185d2b1cde165fca93e9e87cbe80335db4e..a0b996743d34d071eb98bba4c775b8be0bb0bbab 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' @@ -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} @@ -22,7 +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/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index c4932d395387365c8aea6d9def5215cb012e01f5..ebd814c54e20de1a61f89ac4c020a312b8a76114 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 3745f65f5f01f2dd6524bca9ec5d6f4560197c2e..2902acfde69bc63eae271ae901248356711fa982 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 +9,9 @@ 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 toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -31,7 +30,7 @@ files_to_copy = [ 'R functions'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescan_%(version)s'], 'dirs': [], 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 0dc4a540af75aeeb1671168000928c0badaa7da6..0d368866352b7f1cf545f89875f3e7467f89d1b0 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 @@ -4,24 +4,22 @@ 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'} +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' sanity_check_paths = { 'files': ['bin/BA3'], - 'dirs' : ['bin', 'include'] + 'dirs': ['bin', 'include'] } moduleclass = 'bio' 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 2490a42529e66d8b37280f1ae621bc07c94625a4..b13a4f194618a15d22db83f3f8eefe36eb4a0ff1 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 new file mode 100644 index 0000000000000000000000000000000000000000..5bfa2535aa2aec751dd80219a5f6b90a377857ff --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -0,0 +1,31 @@ +# @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': ''} + +sources = ['%(namelower)s-%(version)s-dist.zip'] +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] + +dependencies = [ + ('Java', '1.8.0_121'), +] + +cmds_map = [('.*', "./compile.sh")] + +files_to_copy = [(['output/bazel'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bazel'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..283940594d7ebb1d8ec9c80f888e229344ca1242 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -0,0 +1,33 @@ +# 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': 'dummy', 'version': ''} + +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', '', True), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' 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 5afb842c806f0011366ad25d2fd7544e65143a85..ff35b3fe93f4dce21b527e393a1c80053b4a5d83 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 9d064dae20430ed745791509ebf355d9d5b0b99c..0f2dfc080784f5b24e12fbced9380f84aaf01de8 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/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 0000000000000000000000000000000000000000..b413e97feef8edb429439b6820d9d538b62af4dd --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -0,0 +1,27 @@ +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-%(version)s_configure.patch'] + +builddependencies = [('Autotools', '20150215')] + +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 0000000000000000000000000000000000000000..735a5b6d0ce1a0e63b48ddbcc45d9d7d1d27dd6a --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -0,0 +1,32 @@ +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 @@ + 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 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 0000000000000000000000000000000000000000..c614af140d91fd3258bd013a049cbf02a27d2734 --- /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' 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 2661f0fe3802997d2a090e9cd5bd129b4a06a9f4..c32f54aa1d71b43bdddcf478c6a80b5a69153083 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/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 0000000000000000000000000000000000000000..d5d219aba4af97ef31d67cfc90fd317ecf21ea40 --- /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/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 0000000000000000000000000000000000000000..43055f9bb97921031be594679057146a1566b92c --- /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' 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 a3dca17749044c2d2dbbcbb0b641dd26b1d1044f..26ff0e4f6ad3a87b0e5b46cd7267b7b431cade23 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 5efa64f0e0b39bd4ac7c2fa8a4df92ab46a30d76..462ab92f171c42d90505b512de5e76f6bdfa94c1 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 a42f248efeb46bf4dd8e0f662f640fcf7dc6273d..c5aa94f58c2551f02c755e76edfea8a9db16af49 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 1c5fd3f356ca289c9b3e2e51c73432d62d9d8f1f..f5a410bf2342e019150a266f247baa53b7842186 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 953304846ea999c7fea3c7769546c37127498be3..762f84f5589d192de63fd4364811e2b71c2a5dfe 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 b22f51705c3c532edd50b5307bd25febb98e5ea7..36d03b946c336e6aa35fa89deff47ddac95625e2 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/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 0000000000000000000000000000000000000000..76ea1be8431297b4de10f94badfff0150596ba1e --- /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/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 0000000000000000000000000000000000000000..33d3ae47a6b4891db3c5e3e645f95292b6a0648a --- /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/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 18a7a4b74458a4b3750b6162faf0665cf40002fe..24c748d95f08aea25f52e749f1ed72d5d7d5087c 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 @@ -18,13 +18,13 @@ pythonversion = '2.7.11' versionsuffix = '-Python-%s' % pythonversion dependencies = [ - ('bzip2', '1.0.6' ), + ('bzip2', '1.0.6'), ('Python', pythonversion), ] # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' 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 822d74b107331b20a796e205a66e4f05538da643..0ac767fef8d0e11032235782505a4bfb4046a73d 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 7840698ed46ea38b18c1383ba8780af0f2aad86b..526e2b54e16bc838e2d222f5ff52707c1e733dc7 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 015aad27165b26a87deeffbb317a82fc49b8ee29..918d0a5af6f08865b70522d2435a4ad2c842bc75 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 67f6199614993f617b8c8a36636507a06b2e09e1..d76c8ae2bc80c6bbd057569c938a509ff487e9d9 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 0000000000000000000000000000000000000000..f7ffa6aa0d122120b40ba5a9ec7a91f4f2f2fc43 --- /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 8f216753289eee5e5e8d918aa890ef352944b435..f0e124ea497600af1620c6b0cf53f08ede4c7a1f 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 new file mode 100644 index 0000000000000000000000000000000000000000..faed7a8d9c6ba9d0b74b066ed6a6d80f8a21933d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.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': '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-1.61_fix-make_array-icpc.patch'] + +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-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 0000000000000000000000000000000000000000..e0340fc524efc2598fec5f09d51cf117e0b91644 --- /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' 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 0000000000000000000000000000000000000000..981136de9992379b7dae9c18132ad484ff8d33a0 --- /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' 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 0000000000000000000000000000000000000000..eeada6c5acda24e06e1ecfc631a753f510d5bc39 --- /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' 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 0000000000000000000000000000000000000000..a59e6f69ac260a6784100e94d059d8a439060ed3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.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': '2017a'} +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' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch new file mode 100644 index 0000000000000000000000000000000000000000..b2b7d467a3c91c6a52b6df25a0f501c5dec5d1ce --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch @@ -0,0 +1,16 @@ +#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 @@ + + 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 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 13ddeb08e17c0524439586898d40447635704dd8..f334c5a116455208ab97f29ca185909e7ffa72bf 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 7f8fbd5ca686bb401efd6678973aad32f8813a86..fa8a4e145b6a09e6eebaeb26d0b88e42e1ff84ba 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 361932b89cf66fc3f5e5770f57e65e6cb6a55e1f..a81247d55944260a4f373c31ad2e3b0ea3a99ce9 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')] @@ -24,12 +23,7 @@ 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'} +# 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 02e855be5b27e6d8f6313193ed50d9f4263c0ada..00cfc5cb069655742bcaae77c85a770c0a5831c7 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')] @@ -24,12 +23,7 @@ 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'} +# 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 2877853840d364494895198b049256e992708cba..8f006d90549004c9cbc0c75a50d6a98abd8a70a5 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' @@ -16,20 +14,12 @@ 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'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' 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 975220fa3469e3dbded69fddec56b13deedc8be6..de611ce79f9577620799dfc76ac41d1a3639d455 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 58e8cf38d8d26c879d9eb9cfda92c19341882cd5..9dc4955f2b7587597f1f945d300b3f2de06f458d 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' @@ -16,21 +14,12 @@ 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'} +# 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 da1514917367898ad7f3ac7885c7419eedb5796d..535fcdd94e58d29be61cdb9cf729baeb6d2cbb6f 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' @@ -16,21 +14,12 @@ 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'} +# 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 d2d24de2f8d4b4eac0c411832f82a7a4fc368771..8e2370c31641b3b52c391ddf293ba47c8b375ad1 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' @@ -18,21 +16,12 @@ 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'} +# 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 3f05bda0e89e6fb5679cc28b22bd04e9bd1bd02a..b011315af876b75c340839b9892fc041d5ce0027 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' @@ -18,21 +16,12 @@ 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'} +# 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 d7856c8fa20670e694139de19c6d38b48ba02455..4dca70247f1ee2423a533c365e7f5a8aca77de50 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' @@ -18,21 +16,12 @@ 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'} +# 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 a342fa3e4d18f5e43bb9baa634c6638afe1202b5..6cd8cef8b8fc01a23a5041400aab409eed04947d 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' @@ -18,21 +16,12 @@ 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'} +# 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 3901df0ef725f4b10f4f9f78320d6d60dc52194d..5c6e44e1e9be74931198d04e2a96ea9da0a72e95 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' @@ -18,21 +16,12 @@ 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'} +# 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 f74362241fd85404a2e6f5cccb0b4f4d2a13a5f2..7cd080fdb1497013490b8cc7c6dfaf972dfcc42b 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' @@ -20,21 +18,12 @@ 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'} +# 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 29bf068b6a79690b5e927f38a324b10edd666115..e6c1bebf90f382bfebddd33f8a96b008714e82d8 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' @@ -20,21 +18,12 @@ 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'} +# 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 e48888855ecec82e7a43ed845c0965f2e2390ab1..4982ab4d19ef1a0c29529078111065e3b3c5a609 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' @@ -20,21 +18,12 @@ 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'} +# 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 63080d8ef9d20b9ef66d6a5c02446dfb368cea2f..cf2e82b71cb50db2f25651ea6a59a4af0ac119dd 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' @@ -20,21 +18,12 @@ 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'} +# 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 ab9ee385d74b9a703f0820e4e71d0ea923a42afa..637e625710364c397080be199bf57abe126f5eb1 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" @@ -20,21 +18,12 @@ 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'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' 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 0000000000000000000000000000000000000000..826bc88a15243d9eaa185993e63ae7d86695851a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -0,0 +1,30 @@ +# 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 + +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'} +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')] + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..2526494ae824130d89aec40bfc356635a279533e --- /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 0000000000000000000000000000000000000000..e2859dd50576fc119dcbce65c788864fa5dbaa46 --- /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()); + 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 95d2b2fb64d59d69068ce6424ce27d9083f7750e..bcb89c1b4e3deb4d8be3cf57e917b2c729315690 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 d23fa88f5772ac64dd8e2190914cfe2365747c83..dce0112a41f75876718c0949df5a9040052ba579 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/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 17f6d6b14b75f8bf83b8e758f071c5f6cdf7c2c4..738e6ce0b14847783a8938d87b43e02a20a176a5 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'], 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 29785ed5e61f15120787c76c6b0da2b7d58fc09e..49900e22033bebafa9af7860757b4f544f82b1b1 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 ba27dc855d3aab79bdaa1090fc8c16f2705a0ea7..eb31afb55183fb77029a4e145c4e3016bdce4d07 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'} 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 0000000000000000000000000000000000000000..9346ceba7e7ff4e2b9e1370b7655ed87ad09124d --- /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', '1.2.11'), + # 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/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 0000000000000000000000000000000000000000..de910489db7176b789252b9a171117e40414ef79 --- /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' 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 0000000000000000000000000000000000000000..10ecc14d7a44a73b24dab4fefe5875d0b9fed8a0 --- /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/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb new file mode 100644 index 0000000000000000000000000000000000000000..7681d5cc1f560b3934cf315ce503aa04b9461ce3 --- /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/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 5bba6900603009a935a6cabd625f9265470dd4b6..85e23a5ed918fd1e3eecb4e734c55b93a5a178b5 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/b/buildenv/buildenv-default-intel-2016b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4e742815d335cc7f1629543118a8b0a768945af1 --- /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' 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 0000000000000000000000000000000000000000..8f02847ea1336e5ced04065ae9977f38618d7cf3 --- /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/b/byacc/byacc-20160606-foss-2016b.eb b/easybuild/easyconfigs/b/byacc/byacc-20160606-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..93c0899ae19dc3d3e1750a5c07ada51a3719afca --- /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/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 0000000000000000000000000000000000000000..139b8c3f30addebf7172fece224b507336ba27a1 --- /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/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 0000000000000000000000000000000000000000..5ec3bbe0cb278e1bf8fe3e28a58a348a0f0ee37d --- /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/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 0000000000000000000000000000000000000000..741d95b54532b47b57dfee212991602a14564da1 --- /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' 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 8c90ec640b0236d20dc1748b65d5070891dd4ed2..df0d72298b08d57fe699b730f51d88a9a704507d 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 9a156bffea04a2263263911b14d5d9df343c7e7b..79b1be118dde10e412dc1bfd1aa8d3bb709c1140 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 bf8fb571c8d7adb1e5e25fef20acd59d7cb94dde..a6a8529f92a78de1c0494a47b87ab3a72134dc7f 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 acdf7bfb8dfe1dc7b3db02fd80b42a9d17d350f9..b205f7fd1fbe0752767ad1918ed28cf725f74686 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 177bb20dcc1286cb244bace7ba4155d63eefe745..32bbb18488e0706da7a0e5b20b4caa0d6f283811 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 08e0bf1795b3ead089f732d0ea3223d2c6e7dbfc..32720c1e1c085cf5b844f197ec89907aac36bc39 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 654a6284e8fedce41ef4852e3ce08b399e6b750b..4ea772d549a7667ad64b9c3b7ebe6e4ca70b5a2e 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 6291c9714715cbfd328e7d5940c8f7bc6b4c9f82..d7830dc6332aa687359d4202ef367604db30d124 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 = { 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 0000000000000000000000000000000000000000..382c9e206125a1b1fdf7f2eceb432b3f74c1439b --- /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/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 0000000000000000000000000000000000000000..9bee4db9aa4a506c64639161952a6ac4a227eb8d --- /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', '3.6.1'), + ('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=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e392edbada0a63a470b6851b86dff04e1611771 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000000000000000000000000000000000..e83b067d66e7d07b7645d1a37dba6bc728946c1f --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.5'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), +] + +builddependencies = [ + ('CMake', '3.8.0'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$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/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 fbd1e0f85d8b8f54020e71169da7cb01bb47f8eb..137bbb160376545515e66de5d1c178325f7d18aa 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/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index e6f905f4098a3847b4fe46f1617f55ba6220dd3c..b5f1d052ce6b2774f5500bffedadaebc84a97519 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 130d3553bdf799008ba38f34dfb603f1ed489d6e..bbe947dc70dab642b0b69232e1c85e24e23f6b7c 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 5e1447f0f0fab7b743fad920befa5282f21791e7..e4ebb6e7110c30d07b0147dc9853c0c462f0d198 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 135315981b18ab989b0b3e40cd6886b291610099..c20cd926c3e40fe0a0f1f89aa1efa4e185ea5648 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 b8e7064fcc563ab912f7b9fe48def82c5ae4b35d..86657cbc548d106e6e6d47c3866721c735d3264e 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 86f4ad56814d99e8a4e1ede147df5cbb9f619847..b454e2d862045a76604b0e5dec7df324f3502475 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 635df8455b8275430d34e4ac9950897d90c9a320..a7b9c8e81a08a55fc75b67e7e0f68c6c1e7aecf6 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 ba3ca2e1aa50f78fceb673090cf9999dfb8779e8..4e830d782c9520b723d9c97d6a6d8476dc015738 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 21bbc29383fc1d0ef193f44195d920f10a759cfd..db836864c08cbd5bca5791ad2baaf079cad7de2d 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 @@ -12,19 +12,19 @@ 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'), # 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')] 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 cb117db3226d4a7d5c796c422ea7ec9d2d8cc35e..8b223712ccf2fbe97a70ab4695c2012af0376255 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=$EBROOTNCURSES' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb index 1a599467bd455977ac991cd3adcb113dd1b5ac49..cfb07fd87dbe87e847b285dbfafc63c01598aecd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb @@ -14,19 +14,19 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [('binutils', '2.25')] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 4f9c1dcfa2ca5ca1cdfd6ba248f226d74380dd0c..f268f237cd2637b29bae03471a027b2fdef1b5fe 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -21,7 +21,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb index 5702e9976db58d9e561616805e5a771274befcc4..ffff7b421bca85fe3f88d186943feae03441ba4f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), # 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')] 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 87dc8ebec4ef0dca2936c93194536d60b38f6340..ee7d8242e7ed4c2135cd3867e73a317b5fa97bca 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb index 638514df1f68638104ea2e06ab3a75d2d6afdadc..3b85329fd7b6b56f4028aa2f26a26fb0ec56fc25 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), # 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')] 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 df5823de42217612725d39f3c8cf7901504e638f..c2e052b35661cc4b7b9a8cdb6927b7439c422853 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb index db841bbaef4d9b13ca4b89f411d499d3f268c879..8a76e1e7924f7c826016f9940d0a102725d3d64a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 0204c038c79b1d9b90acf1cda613239af202f760..88f897fda1fb75e9871f4a066b9a18bf3883be91 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb index 36a239c230c516bd3d7d7e5f31748393b84686b2..1c3334739a849084ea6de839a83334228dae6fe8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 e6beb92beec75b68d631264600ddc139f381db97..3abfe801d8d9e238fa204ea81fe60f114882694f 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb index cfb29da8c6bf080ad09d850d55b07d4ee2204841..4f47e3e9af7172913815ceb501a2c859c62a9224 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 f5527c16d6f57b6b93f03667371009553e590f1e..4d2e8c78ebd37f0c6886d9275765a5fa4727a952 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..7ff969cd255ddfdf8901053f09e2d91f24db4577 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +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 ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = '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 7deb175b910b133e3379d1db0991272376d43082..4c6f13f16c564a864e3337818f84fde6520912ad 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb index 31b70f1b8ad9103d977bedd2830901882b501e41..e2aca6e62bb29e2202c9079b5563914759b3b7e8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 c7cd4a579a0fe1ef1143b43f99f52c26067d9e4c..9ffba8c3ebe2332b199c1e66c41e092855f41e66 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=$EBROOTNCURSES' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb index f9e868c77a7d018860f5ff43b6614fb56bb02632..38d4964aee3c2b8d27064c030d5bab0b3dc66780 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb @@ -13,10 +13,12 @@ toolchain = {'name': 'CrayGNU', 'version': '2016.03'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$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 a70441375c0e4016fb4660ae26409b92fa93be4b..f983c4cc8dc5c64bee375664452b1865fdca3c63 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 619aaa3ab8aa293ee5a423bca49653d6debe769d..b10a90630e95b00d5a9f25995d8b3c74f30401d2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), # 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')] 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 9075c094fb9dddf47a7d3a7d009235ce8088034e..ac3c18045c39eb43f999fa230a79ded0c57238a0 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb index 42e9b3b3bdba0019e6715258f9e557f63d0cfff4..7752fb3e02a67adb508b5886e371328b5f190aa8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 1f3daa3224c58476a6109ba6ba8ca96a5f162c5a..d8e716c6e8c8e231623c6de33631e532deffe032 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb index 6d07f31ebd4b1a43e755b2083b42e9d8d54c391d..58e3a733939c1a842cf1fd783db08368f26602d2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 b68274e5b4bf4d24e8945a31d3df4c4ca653bb1a..bbd6da6d24b82d248506fa95bea6b5d07b676da4 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb index 412e055df687a82606c730b5edd4c317f7958305..701830e8719d0a207b3455b4383aeb95f3cadef2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -12,10 +12,12 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$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': [], } 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 97b2282312fdb2dc386f319eb008d3f7ab5c60c3..d75cce9d86666ae2ac630978630d7ed11228b897 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb index d5ca429e05c505cb75fa5bd613bb898ff5121bce..24218f54654c9bc9fb744c62740e02429220eb94 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.25'), @@ -22,13 +22,13 @@ 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')] 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 c1386c78f896d8dc07fb578f87f9d3f0253b1a5e..6d2b9fdc586b22936bfa284a1fbad0d7620ee47f 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb index 40d915d152ffed6606ba6cd6a87ebb9e652c2944..f670d07d54588f6b501dcc7804bc2f55bef74639 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -14,19 +14,19 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s-use-gnu11.patch'] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 aa63de70da721013fc93e04d1b4e4f1999961539..270ce1c1354d642ab4a769de0224f226ad5bcda2 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=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.26'), @@ -23,13 +23,13 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb index adb0724437a111d40b93466730dc87eb11286f72..70548108abf16b18e6223670628528200e518d81 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -12,19 +12,19 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # 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')] 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 b6e496837c29857c60970db220b2ab962dae18e0..f06386cba38f113fd70774eacf8396e117fd0212 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb index 5b3221d0bf7e2c9e09c6d665aee8474b1aa3f8cf..c650526070f2804dcdc9788d9a5cbdc321cd669c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.26'), @@ -23,13 +23,13 @@ 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')] 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 b364332ea03c7dc74cfe573fcdba9bbe21b4cc92..99526d7cb2d7492e582493f520beb7760b9dec05 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=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), @@ -22,13 +22,13 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9bbc720528b1fefe60a5da8006d328747329facb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$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/c/CMake/CMake-3.7.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb index 0464c9024de4e98f9916c5b7400d9a2a9e92d14a..f948d565bf8ce80b0f8d82b50e111bf838f15071 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 @@ -12,19 +12,19 @@ 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=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..29e1e466f95181a9598b908a785ca089687e746c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$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' 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 0000000000000000000000000000000000000000..1d41f93b9bc373ab7c1f70769b377bb2159372c4 --- /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=$EBROOTNCURSES' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f113cacf3eb4c278ee0e9b8708fd78402e3f8c08 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$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/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 0000000000000000000000000000000000000000..522448447cd0fb41baf8299f2764b34d8199df1a --- /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' 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 d34361f252da6988dbf91cd954686d511960a5ac..bf60245a75e7a72707e96bfdb9a345bb7fa80c92 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 e7bf9550c79da598cb2d9b577d8545be2d804677..20bfca4976bd98ab6d0cc7afe939b37c3a2d4dae 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/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 0000000000000000000000000000000000000000..f487ac6f42914c6a351b6e59fd89304414d4e5d1 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-4.1-foss-2016b-psmp.eb @@ -0,0 +1,42 @@ +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-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '2.2.3'), + ('PLUMED', '2.3.0'), + ('libxsmm', '1.6.4'), +] + +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 + +type = 'psmp' + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' 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 0000000000000000000000000000000000000000..1d55051d0c458855d6ee29ffe71b7995437af162 --- /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', '2.3.0'), + ('libxsmm', '1.6.4'), +] + +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/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb index 299410b70c78ed6b7fc80e299e0883408606fd9a..8997152413faa85db8140f20f6cced33c0d4b177 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 9b2a072f8b8b668acd1594415a83634eec62a8f2..194a2991a96fed6eae335747c6363a930ae4d036 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/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 f2ca68b5c14c5f44312491f6fbbc352095c74be0..45b63f03802af0d912d6bf234f78669715fdf960 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' @@ -38,6 +36,6 @@ 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_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 8ed8a29bfcb7c7cb6ce0e1d4d2fc6eaf397f6e7d..72651d5b5430553ccc9f96cedce0c96c36dc6ed8 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' @@ -38,6 +36,6 @@ 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_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-8.0.44.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb index 9407a6399ef7ef14f54055fdc14fcc962d13f60e..8a34ad1f5e226c874021dc1b82ffa891b194e34f 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/CUDA/CUDA-8.0.61.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3ad585f708a484ecde5b1ab0f8add8ee615ef22 --- /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' 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 071eb0169f78ddcf0a759da9cb836e698c457d10..e06141ece538f88d3fcafd86e39738f86980f4a7 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 3e32468f92e7b5a4e399b96b79251bb3b7c792ea..795f2f0360453c76006597800b6e856a26261fdd 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/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 new file mode 100644 index 0000000000000000000000000000000000000000..4a545a7291c3aab999d3a153181b39d690474e2b --- /dev/null +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -0,0 +1,59 @@ +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': True, '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' 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 df2115bf2e20534ea02b491090e5877b22060915..6ba32558a29624b78bb7146880cd656e6b635a01 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=$EBROOTSUNDIALS/lib' buildopts = 'build ' + common_opts runtest = 'test ' + common_opts -buildopts = 'install ' + common_opts +installopts = 'install ' + common_opts prefix_arg = 'prefix=' modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..87566ca1da06d829a99fc3ca9d2293a7d832767c --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,50 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'Cantera-%(version)s_fix-bug-416.patch', + 'Cantera-%(version)s_fix-test-reprod.patch', +] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('SUNDIALS', '2.7.0'), + ('Eigen', '3.3.2'), + ('fmt', '3.0.1'), + ('googletest', '1.8.0'), +] +builddependencies = [ + ('SCons', '2.5.1', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$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' 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 0000000000000000000000000000000000000000..62c745b3534d83bd5a17b971f7ebc2c8d3668aa6 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-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': '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_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=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 +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' 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 0000000000000000000000000000000000000000..74efe309f7e07f3bcb2a814518ae098c99a72c1f --- /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_fix-test-reprod.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch new file mode 100644 index 0000000000000000000000000000000000000000..83dde312f8df6ce0efba5be00911cb6cef0fade1 --- /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/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 eb2d005b6fe33719b6abc670e00d1c3d450e8cf4..b0d7e2e41b23da175a7e8e513bf6b6d16f212f4c 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 @@ -15,9 +15,11 @@ 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/%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 dcbe783b38e9c51a8140d81bdb4c9bc7ef482533..54bfcde59ba8a024b8da4af6bc770622f17b2468 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 @@ -15,9 +15,11 @@ 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/%s/' % '.'.join(version.split('-'))] sources = ['%(namelower)s.%(version)s.tar.gz'] +checksums = ['e36736c5151c872d9fc7afa54e3e8ccb'] + skipsteps = ['configure'] buildopts = ' CC=$CC' 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 0000000000000000000000000000000000000000..bc4ee7373595c8b7eb775ae604c622e59d02b618 --- /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/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..26131a57649bcaab0333681ac0d998d9fb16319b --- /dev/null +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -0,0 +1,26 @@ +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] + +dependencies = [('PyYAML', '3.12')] +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' 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 549296f08e8118a595916f2a733b3415255e9de9..4000cc8571db046618348affb032b6c8031ce500 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 @@ -1,32 +1,32 @@ -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', 'extract_reads', 'filter_reads', 'index_and_search']], - 'dirs' : ['doc', 'include'] + 'dirs': ['doc', 'include'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index edd7b1aa5d438fa484eeeb292abee18039b767f9..fce250c7cfae4b56a166207f7b859d240413fadd 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -21,16 +21,15 @@ 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 = { 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", - "bin_rh_linux64/wb_view",], + "bin_rh_linux64/wb_view"], 'dirs': ["resources"] } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 112a9312bced57dab986f2f79a1173329d09ab43..8f554a1eb2ffbee46038719b70a1bbfe094b5eac 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/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb index 2facea57d93b5384a34e9b880f0c3713c743f78c..e56c03bf3f1b280a601966971ce362c914ddfc83 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/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 fa53744e7cf9e2d8f6e95ac9b91dbf1ab5d359fa..e22250c9905eb7150f095d07d7df3406c95da91b 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 f2fb277465351094a29d872b7aad9cb251ea1595..33b4c1bc5be0a4846589da14ccb2c0be0f145b75 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 0e8ac631d070ab4b108be909cad85eb9385f3f45..ec51d696a0137f855dd35eddc99048c34f3fbd19 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 6ba8ee3375981af9f61ca572e34e6c4374b53adc..1cdbf2c1fc7bdbbfb0af53d46ef70e8e5eca25c6 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 80955e4cc6f9e1ebb87cd0ebab3b65cfcb149f7e..8494b353e53ffb516059a65fd1ec99740916ac65 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 1a87b1c99cc3d154d19ba8e26dae0b4b83704562..769f55ce72a900a769d87693e43270740ea43211 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 426fedf887289d59bfe82e89e8f88134eb524dcd..dd9fc1ad56a776942a81ed031327222f4d3474c0 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 a2db0bddbe99132238a4d27f2a5214262a4b4899..0dfcb1056b781afc1eb6ec20f8187df133fc8abe 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'} 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 0000000000000000000000000000000000000000..669ee4f2beda8add04a1d76bbf5c17d3bf7c5bfa --- /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=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..09811fccdee50d0ffc63db0a93e69092e99ad7d0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.53.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$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/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 0000000000000000000000000000000000000000..8d7f087e2b7f73632248d23506a5090081b2f71e --- /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' 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 0000000000000000000000000000000000000000..39aaca6d60a7fdce4266ba618a067dfac8a9f8c3 --- /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/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 0000000000000000000000000000000000000000..872e069d81e4edae4f96c96fa910856bfe65775f --- /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', '-libpng-1.6.29'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('X11', '20170314'), +] + +# 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/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 0000000000000000000000000000000000000000..fe63f8a29c952b985097e9df2fff31d8a93f69aa --- /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' 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 8172078525f96c03663a1beea13b87ada0cd6e0c..f9db925788875c6fd0391c3647fc37f8c1496884 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-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 0000000000000000000000000000000000000000..5bd3d25aab67742159c49a1a4f405e85600a64cb --- /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/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 10fc57629790cf1dc3e8f3dbcc5c8fb3e6bbf443..bed63bcc08711b5c5c7e721001efce4749208992 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 e3bb6d9e200c45ba9bcb91880a3672f3896906db..113e88c75f7e9930f9940e8350ca0431bdde9d62 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 0000000000000000000000000000000000000000..6deccec5e63c1766f51240c58e5d53b3a8da7d36 --- /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 +-- 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 d2027312f5b2b01d8454d75ed22887c6272eb205..5f652c0c865e556b474e311ac09e013bee0ec63d 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 $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar\n" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb index d00a912e71a5b69f94d1ffa3613d19925b4b10d1..a560b37abe787c56e68fcd44563c08b05a835e41 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/enasequence/%(name)s/archive/'] dependencies = [('Java', '1.7.0_80')] -modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" +modloadmsg = "To execute cramtools run: java -jar $EBROOTCRAMTOOLS/%(name)s-%(version)s.jar\n" sanity_check_paths = { 'files': ["%(name)s-%(version)s.jar"], diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index c378da306a5e28ede1a90393432053ef32fb3224..60152e7602ae438bc42f8e51b770499f6262044f 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -22,17 +22,18 @@ dependencies = [('GSL', '1.16')] # when running ./configure in the root folder it fails. # application doesn't provide a 'make install' prebuildopts = 'mkdir build && cd build && ' -prebuildopts += ' ../configure --enable-static --disable-debug --enable-optimisations --enable-openmp FC=${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'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/ctffind'], '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/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb index 0cbdeea8a4b08547d57e18988bf612673de6fcec..08976a1f68f171699cf1208de0fd2dbae77a8b08 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 = { 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 0000000000000000000000000000000000000000..942648ea47a34c4379d17330b53738b3afaa5a84 --- /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' 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 0000000000000000000000000000000000000000..0c065c7d55a5066fae6668a21a4c8e759f86ef52 --- /dev/null +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,39 @@ +easyblock = 'Bundle' + +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'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('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 +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' 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 141aedc7d3d5b009aca935d9680ddb6a708ba2af..2793fdd39051f4753383c0c4a9e70af28e5a7bd2 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/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 5c57e5846c2a39d70bd372c02702812bcd8d4c7e..99d5dfa45cb48002f6cb0de3fd99efc6b5aa80f3 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/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb index fcf1bd769617b093b3eb1824ad17539b52004e91..b1a5625761517d7c8d5d86c0874ae2c0e051aa0b 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/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 6491ebe755614488ed5bca43b4265b1e3da6b7f6..81827042d8f0a05a3eb7cfb46b8ed43c64360365 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 0a65c07d0ff3d66afb68c94c5c8f90fe9512b0a6..d5862a7c5a92c8a5d5fd9cd2c9d919377f313c24 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/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..82d644aaffb3f6ed5c94baa1c2639778d508d06f --- /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 $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..367145a27380fe85db3e305e55177a42b6f5e5ff --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' 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 8c069fec945235589e0467118777b76be9742c9e..03f4831acea2bedf6a81d519575753e8155f0035 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 7071afdb2c399a237e3b67f396969e2547ad2fd5..2a15cb846cca6d9a7d3769865a94b52c0655db03 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 0940c66fb5b827ec733ab871720e5d2598efe97f..7dab289eff39264e2a8c0206dc58b957abcecf4e 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 f322881382fc4ad293ba4d60f7249dc3baf08b41..e221d7bbc5c84eb94829d09e08664a2c7c9bc5fb 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 99e680c26db2e91d3c7e82a59a71ab8d66deb3e4..389f7d842523d4498ac6fe5e14a0873bc2670915 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/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 0000000000000000000000000000000000000000..7f8e07f3250e3026c8e93e6a8b2dac8c5f95428b --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -0,0 +1,43 @@ +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'), +] + +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && cd prg_dftb && " + +buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " + +files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dftb+'], + 'dirs': [] +} + +moduleclass = 'phys' 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 0000000000000000000000000000000000000000..19f96d592f8af9b6ebf3af1b1590d1adb5e62e8b --- /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' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb index 597de0792e7d546c3e3d1d78dcf9857d0fadbb7e..04e4fd7a51b38fed6e7cecb2d41936455ae7757a 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 new file mode 100644 index 0000000000000000000000000000000000000000..1687e9b44d4c94e5eada1b2d3161de2ad2f996b6 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -0,0 +1,26 @@ +# 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' 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 295844b8bab62326fe432853ee68d7d20fb9bd1a..5106c4165f971af9781a2a65015785d2f4977e0f 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/d/Doris/Doris-4.02-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..37cf20fd5b6fb51a22ee2b22ff2fca0a65dd78c1 --- /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' 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 0000000000000000000000000000000000000000..00e9535d4b0b6efe6d3c0ed5ded60289c1c7cc0c --- /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/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 0000000000000000000000000000000000000000..f639521510b6c87eba4896c46ce23c7bdd05b289 --- /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' 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 0000000000000000000000000000000000000000..7de0a8ea92b477766bba4f46be37401fc79f0bc0 --- /dev/null +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,42 @@ +# 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 $CXXFLAGS -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/' +] + +# workaround to avoid the import sanity check +options = {'modulename': 'os'} + +sanity_check_paths = { + 'files': ['bin/disambiguate.py', 'bin/disambiguate'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index ed4f3f692d8b98149c0fef35c4b0d9df3e8a939a..3d7e8e50d6cf192cc8bd3fbbec01c76237b3fdc9 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$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 3f01a8dfb96f0a4516cdd5e3f21260cca03174aa..33794a918dd487b17c24c5cf197a4525c5d6389d 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="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ba1a5a27b65177cdfabcc2713a4da112a0ad242 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' +versionsuffix = '-serial' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$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' 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 0000000000000000000000000000000000000000..eed367500a64329c6f47d345843a15cc1ec75aa4 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -0,0 +1,39 @@ +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_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=$EBROOTHDF5 PAR_LIBS='' " +buildopts += 'F_COMP="$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' 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 0000000000000000000000000000000000000000..4f73ca348705803e46ee6f79954f7ea7980e69b3 --- /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 0000000000000000000000000000000000000000..601e93e788260ffd71e526c0cca8b5390bf22d8a --- /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=$? + #------------------------------------------------------------------------------------------# + 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 6b962c6687fcb9fc2d126c2ae6372045a8536d8f..a429626ec5c92fa89863ef5a08b803cd1947df44 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 89cd537fc7b264a12fc90732f4f375eb70ed066e..c9a900612fb30cfa5393ae4db3cbc215e68ff727 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 ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index bbbc8c56b4e9bfe4f9149b3d0cbd77ac21735920..97838620787634e0ae9535dc94c71b859e6dabf2 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +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-2016.05.004-intel-2016b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b188df034a8a9aadab7b836c52ff9cbae2d72f23 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb @@ -0,0 +1,35 @@ +## +# 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 = [SOURCELOWER_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +configopts = '--with-generic-simple ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +buildopts = ' V=1 LIBS="$LIBSCALAPACK"' + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' 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 0000000000000000000000000000000000000000..75d318f6703f42c5199b8126377a3f5c8ea80c5f --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -0,0 +1,56 @@ +## +# 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 = [ + '%(name)s-%(version)s_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/ELPA-2016.05.004_install-libelpatest.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch new file mode 100644 index 0000000000000000000000000000000000000000..61ac3562663366a97da3548cbb7531d4bce0d8f6 --- /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 \ 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 c8367acc3482a00203326be2bb66eb59851f8639..573a00a1859911f14e0e5d2ebce87015a1965605 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 88380bcbaba3a92fc7b063101eed3f0c92230040..cfcf1c4b41a7af119a5135715d7a1d5b27a6691d 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/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 0000000000000000000000000000000000000000..0d6ccf3dc761afb2d75bc4db2d3e8a9b6f782652 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -0,0 +1,48 @@ +# 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/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] + +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/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 0000000000000000000000000000000000000000..fec7e0e3f7605b815b65161d90e4941b6db4a76b --- /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 0000000000000000000000000000000000000000..62a98e0354d19392c70396a17a25f4cfc1f96733 --- /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/e/EasyBuild/EasyBuild-3.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..606f9a318dfced64f050b5906fef21decb35f4b3 --- /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' 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 0000000000000000000000000000000000000000..2dbc7fa9badfd3b7a3a5e91d4e5d90237fea708f --- /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' 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 0000000000000000000000000000000000000000..eaadea3b41b4a014f04102daab1956a521fae5b8 --- /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' 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 0000000000000000000000000000000000000000..d84e16eaba5b6fd5d164df6212fb9b205189e36c --- /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' 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 0000000000000000000000000000000000000000..9ec07e22e9141c85de54f0f0005877b3bef98e0c --- /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-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bab8954a19aeab495bd69ce929b25fe478f9721c --- /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' 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 0000000000000000000000000000000000000000..6cf3aabc3c62b5437cca4c44ae1cc618076d8809 --- /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' 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 0000000000000000000000000000000000000000..86af55ba48a9616ba2592f9ce9f3fd572f8a492d --- /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/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 0000000000000000000000000000000000000000..fdeb038ac87e78735db875a813cec8311dfb829a --- /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/e/Emacs/Emacs-25.1-foss-2016a.eb b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bc3043a68b928dfd97bdfcb3e577df21bae3cb7d --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb @@ -0,0 +1,30 @@ +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] + +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' 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 7cf3821ef383af5885f474a2889e58a3b9f0cdbe..498218ede9550cc6a2c890f9fbb56f176c073dd3 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 e8447b7c643d41508383b06f62954f8c177a572e..5bd575648e76deebba8dc95f1f7cbddd3c3bea1c 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': [] } 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 0000000000000000000000000000000000000000..a1c32a3e346b6579d7d7869c949b110e914481d0 --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb @@ -0,0 +1,48 @@ +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'] + +patches = ['ea-utils-%(version)s_include-unistd.patch'] + +start_dir = 'clipper' + +prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " +buildopts = 'CC="$CC" 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' 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 0000000000000000000000000000000000000000..3fb5b110e0a50a5cf37283799bd489422aa34c91 --- /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 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 0000000000000000000000000000000000000000..a82113c472b6059dde40b1bc62550e76376b7118 --- /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/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 0000000000000000000000000000000000000000..9999a81cbc825e8522accd6d3b166c6f839f810d --- /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' 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 0000000000000000000000000000000000000000..a67bb4fc20de6bc3ab66eecf8be4766e1a333a78 --- /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/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 c1501d5c82174ed3f0a01619d50c7a1937d58ec9..cb997fa5934efb8f4f2281371552b8ec206a4a47 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 6b9a39e112c82c97d32a43476cd3a13a88f5a6cc..31a89c008557728575918bb48ee66e23da553106 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/FFTW/FFTW-3.3.5-gompi-2016.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb index 854d665922a217eadea7bf2db6689ea8ea79cf8c..b4418131e135be45cf4a1a129770223e802752a3 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 95601b61f5bfb09763f66d769050eb2341f2fbcd..2b26aebdb12a013d9a53ab2694c2d1684c30b585 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 e222c97b5d0038b3fc69a5a4e0b300763864bb05..2398a80c24d54d8e8c8bc73fb7eacfb328b7ad62 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 2499d7f87ae01192d570649b37573f584fd88ea3..802e40e5f233503c97e1dd5cebd786c250abd1ad 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 6fcdd25eb53518ea226ff2cd9566a603bcb73901..f931b781ea2da3d8d29a197a14e0b8a53e489999 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, Intel compilers do not support FMA4 instructions +use_fma4 = 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' 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 0000000000000000000000000000000000000000..f09a971da7ad9c8baf270053c3f3c9d90c925ff0 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -0,0 +1,1529 @@ +# 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 +# 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 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 +@@ -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 new file mode 100644 index 0000000000000000000000000000000000000000..ad3e944f8a948c87378fb7b506331e9cca4d9d91 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -0,0 +1,17 @@ +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': 'gompi', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +runtest = 'check' + +moduleclass = 'numlib' 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 0000000000000000000000000000000000000000..2c0fe9cb97c487d244aea52b258f22d2c8187a11 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -0,0 +1,25 @@ +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-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +# 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' 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 0000000000000000000000000000000000000000..7d5646bd9ca1ceba7bc06c5a970f69e7d6e1b6d4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -0,0 +1,25 @@ +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-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +# 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' 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 0000000000000000000000000000000000000000..235a728b8c55634f532b3eddf99f354db26f3ee8 --- /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/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index d7d711211d473aafbd04bb0bf2a34fd72fd3e4cd..aee9c310da24d6e798e93813e239efeac6aac562 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/FLUENT/FLUENT-18.0.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..7feeec83d45540330883268d46b39abb2a589684 --- /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' 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 0000000000000000000000000000000000000000..ac5fcef9e128c045b00419f727c09e2bf8e38ab3 --- /dev/null +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,60 @@ +easyblock = 'Bundle' + +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'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), +] + +# this is a bundle of Python packages +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/'], + }), + ('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 +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 59de3272db0df7ae24fdb6b256e976d343422e17..1788c8a21afc5238123e27e9a84859d1767247b6 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/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 69c610cd3fa824ca2232f9fbe5e9c8de682c8bc3..94b4d8c173c48bf7f53393d6ae9e847393452223 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 0401395acc9e127fe0a882ff939979886d06b220..e2833c7203f714b009a6f8dd40704b88c5958ef4 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 c38933ad4fa03ec8069dfc616171467f17ec934f..40bff9f910381985f84f02cd77e4d5527ade3af5 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-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b7981e18c5a2ef2d8a487aefee9d1be21c6b9308 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-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': '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' 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 0000000000000000000000000000000000000000..2e9b594a70f56850b1de575d701e47a7f4bedb7e --- /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/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 7eeaa4c1a4e9d1d76ef9ef00352410c5e0a66b05..5e8c01ab2dbfb4c8502c99a52cae1390dd2f85f2 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' @@ -20,19 +20,20 @@ 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 ] 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 @@ -46,7 +47,7 @@ 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/f/file/file-5.30-intel-2017a.eb b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cab481c6f4ef11452ec4a66c10ca29e321f308cc --- /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/f/findhap/findhap-4.eb b/easybuild/easyconfigs/f/findhap/findhap-4.eb index 06eb1f492ad91428703d5e71818366c181b97f84..7622374b6656aa31648192e71c9f523f892b6e8c 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/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 0000000000000000000000000000000000000000..fea26879081694443eb365736d418db225e181d5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.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': '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 = [ + ('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/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 0000000000000000000000000000000000000000..e7dd6de964c32e48923c9482a8a8bf7f653071ee --- /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/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 0000000000000000000000000000000000000000..28c855c205d9d6fa43349d7402276067a2f0b823 --- /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/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..568be27f41f425e167fc980469afe6a5d558e254 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -0,0 +1,22 @@ +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 = ['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'), +] + +moduleclass = 'lang' 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 0000000000000000000000000000000000000000..6faff2689b64da6b8eea43928c9fb58e42bd0310 --- /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' 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 0000000000000000000000000000000000000000..38241af81f8ac56018ea5afadf2961ce9baefe6d --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-intel-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': 'intel', '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' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9da643ed432d3693d78e48eb5bf4da6d5b4ed08 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' +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 +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', versionsuffix), +] + +# 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/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 0000000000000000000000000000000000000000..2cdc8b58dea54707560f51478fa39d7970828701 --- /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/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 0000000000000000000000000000000000000000..dc6e546916e8c4680aa9a0b174bf06fb64d9410a --- /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'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/foss/foss-2017a.eb b/easybuild/easyconfigs/f/foss/foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..400c0029a9effc679ec6515d48eeb7900861ceed --- /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-3.7.0' + +# 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', '3.3.6', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' 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 0000000000000000000000000000000000000000..4e2183f308b14c0e53043b7066d24f771568123d --- /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"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..c00d6cd413294dd224d96b4939a5929448fc709c --- /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' 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 0000000000000000000000000000000000000000..9a0faa6f4907f33d167e2b24fc24ccdca7c2ed05 --- /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/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 09e345ac68770efaa66f893035e10a05e4e56aa3..7e51dd88f4568f6acb5c782e0544e8f0d5d4ed5b 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 f0c8e977f83efa56602b057a2636335648a5e0be..bcf6608413cb29275bc7583932ab2a363f63ee2c 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 dafae024b098291bd3af68c3471f0d086f6209d5..916f1302f28c7c603da3feb5bb9b4411556122d8 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 93ed64ef3127e33bdd4d9c1e12ac9317bad17687..26eaffc5f6c6e498c35a450853f8653230983d67 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 c7a87aa9acca1a738f4e83cdee765f918cd54da6..cbbe1daafc85a07b036f294a2a8afdc004b54294 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 5fa7fbc89e960634020edf4e5379515f36058943..a5e70027fab45f3d28f9efe1d5f213743d527443 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 6af71f85bae7577ee876385d1bd82622007fb16e..8fa382b0ca5bbcdf01153d984dc710544db02b34 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 7424371c2999170871b01eaf1de2db21b2df6ff3..0571a145ad22f907ee04a574a6e75a775b1adea3 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 1840f18b99cfba51be6ffc57b88d16b47def8fe6..cea107f292165fe262e044e619fbfd3e3e992b2b 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 cf4ca6186c312c0147657da9b3685f817da2ba08..9b0aae30b7ce491d69e671a29749b6bf4a2d6e57 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 68312d108df26ef060a24d28e4ff22e4e4cbbf1a..45d6dc8e9383aa1602d9f784d69d43d999c9bf65 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 e9f0fd7c959882fdd0ff168845aece4264346cfc..c9b6e770b41fd7f7952a975575a5a8f6685460e2 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-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..773f70da967a4f61fe2d8653ddcd32d1f5a9126a --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +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'), + ('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/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb index 5eb7f91b58423594ee233daee2957a7a58c53b88..07f4f8160c3662738d01a384afe37f24614c4d95 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 ca24a618dc1be131169a1fcb474295c67fab6894..44080cb0f8fbb6a47f77ec7cff113fd8c450d01b 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 89788124588b4233d1d2bcd61db8bf26eee5d509..7cfa18b2f481f7758269f4b0a8a7c67adfc878c6 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 af7228f4f5421469eadbf09220ad01825005b70b..78c7fb98d63ef7d13be2741bee0224e380afdcd4 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 316e040e0881748cf5afce930605f538c23bbc08..4cf88e23a77550008e040cebf9acd762fd8b2d31 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 32b12425a852e0283b685a27c6cd1ca39a7d1771..8405a0ec9357ebb0383917d000e7c0787972ed8b 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 0913227caf19a6b5c571a4e5710312d98f6299af..9c9d2b2e0891b1cde689fc53ac81dcc4cadbc6af 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 32c4b9ab5ccd913fba135742d42e37c7e813dd7f..bbfd2a25088d42067809da352d09c54a405a770f 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 54449d24056244860310baefc79710fc24314d32..912f826139413a4a8bf751c62b9a3c4413ef25de 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'], } 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 0000000000000000000000000000000000000000..7436cc5833e5499e150035d9ff10e31845532b8b --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +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'), + ('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/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 0000000000000000000000000000000000000000..fee6777ad044875848d8d7c93e82d879e59aeb2c --- /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/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..1b0dc16aba5dc05f36cf830d025caee710e4edb1 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -0,0 +1,31 @@ +name = 'freetype' +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 + 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', libpng_ver), + ('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/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 0000000000000000000000000000000000000000..2892f7ffb0e150671477915c2a52a9e9301ff712 --- /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/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 0000000000000000000000000000000000000000..d3a160563e8bf6c11ffeddbf67130245bceba787 --- /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/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index dd2c25a6273d5f3bf74e63a40a1908768e78421c..15da25496f967a156628330cb7859bea1359a68c 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 $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index ee70681358adac604a926d72c27e42aef1f0a9b0..6afbdb7b4c3356cd991e8804a1f61d4912e67145 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index dde93eb10a0faf69de36703c1517e0c0fa89eb00..921621187e4008036eaa483c57c5af55180306e2 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index a45cb4ec3bdc1a0bfe22c1c04b29950175d0c060..7e9f79abb84ff8e2cc1198236f507494bc30e7ec 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 1bdef83c68fbaec7972033a6924a21a41e7a3269..272836da198bc59ab0a3361878938c2128f8d046 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -16,7 +16,7 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] -modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" sanity_check_paths = { 'files': ["GenomeAnalysisTK.jar"], diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index 21448792b2586cf3b6533b9d18d1ded0ecf8e58a..959d6f681a7e8dd996ae70b4ca918a47c38869d8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_10' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute GATK run: java -jar \\$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 38e7ae6db1890778b73f7ac995af9aea865a3ed4..bae4a90d9192a6d75f0fe93d5b8010a0e24b5954 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 # $Id$ # @@ -32,7 +33,7 @@ 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 689accfbd9d1a55c8e429cb48c8d8cd60ea29a6b..88a772e2f89da61d83a2d5ff08ba7c364900fba1 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 # $Id$ # @@ -32,7 +33,7 @@ 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 520cb6b37a67786ee3d4a0181fc388fb8b26563a..d0d5a239b60c58491c9068e5a78de26a262ca81c 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 # $Id$ # @@ -32,7 +33,7 @@ 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 adf96fa7cf2133ef49c2dcc7b77056ce4fc16493..b6d45b10eabdb7edc49e0343e711c21e1938dd94 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 # $Id$ # @@ -32,7 +33,7 @@ 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 c52824dc923673d3c41c8a119ce49b1e28ac8fa0..935f73ec903c0c5b26a71dd415cd9f592b604a0f 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 # $Id$ # @@ -30,7 +31,7 @@ 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 3bbed9824ebf1b0498d618f5ff2d55d8ca2d9ef0..6ed0f408638c910cbc8d35edf93b7b9f870e23f3 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 # $Id$ # @@ -32,7 +33,7 @@ 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 new file mode 100644 index 0000000000000000000000000000000000000000..afc148cb14e86d91ee4e1a14f85d240d1e0a3b68 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -0,0 +1,43 @@ +## +# 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' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 4cfb618383c0d72cc2d1751fd704faed38b37322..8e387e8194deeb2432dcb3cffd514d19c92a1fa9 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -100,11 +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' % 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 70eb5b0a10886b9e2a07d899ba857371fb48867a..3a8e68733e426ee3efa52b90ac06d6beb4ec2197 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -100,11 +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' % 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 477760c3c0eb75e91a9900cf3509af9dc45df2e0..b9b142b82cd6ec36fcd61ee0aba3e29a2bcec36e 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -100,11 +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' % 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 d952c146712437564ff20215d92ecee2cd7bb276..12435392e5269e8d8ddd8851319ccc2d9346fb68 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -100,11 +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' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] 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 041898fae9be81ec8e4fed61e6d9aa5acde12186..618d5530316b16078f6900cb4e9e9c659511ba88 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 91e4497eaa3ab6dd231e2bb082ac752f395f66ef..6d29040095f930ad3afe3c947402b65db9d9454f 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 d6ce9a89a02113ec336fbb9c175675d4f79eb2f9..9a60bde46d3d9888d0f994f4172f0868efd20e0c 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 a5d4cd082d2dd99b8412b653384c7c00238db55c..54f482d9068d3eac382cf149668acb0dff725d4c 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 1d2159779bce34205d43f6c2dc33c7bf4f5d276b..89f13931a3b3e647671c3a0f26dbf1d905e9b8dd 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 bcc4336300082b7fc8249dd2ac7ee16aa1391d22..1fee24d2add5af392da3ceff6bae4b430c4b35dc 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 1293532d231ecea5f29ba4cdcbfe250ff3427850..c0cd444cef0d2b27599d9277f3f8a16cb578ca6a 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 82341a9a29ac9944ea4d4df5754b29cd8d047325..7a4b755a4c35d39c0e9de73b36ac616c72760db2 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 7f03450a91d6c6dadc28f4a9c2ce6c6d45ed8e6a..bd08517bfa637294c6e3a9a17a7f4f6268ff5c85 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 163de21ca1ef78b62227539954adaf7e898aca81..5cb7dc788a8ad35ebceb4a15f4fe2dc4513aad4f 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 323622921da5f3a903b3fd6bdd6091b7cd62640b..4b52dcc3437a66203265dd17f447bba71ba9fc7e 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 b5769a1078543d0594ded3d4238dbbb2ef3d89a3..1ec5100100b6e1f24f0f6356dff4663db1b153b7 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 4820fd10264616e3eeb13b35b9a97731701c94f5..897ca9088c8676e97f5c6b6fd8b05126bdc57902 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 f18257966453036dd089bc6a3a52466fa1969951..88c83fce429b42456ef0ac24970aa579ef5b7673 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 47b8d2c23ba4ce8fb2ae5b3a6e6e36b821d16906..4052ab789be4ee663e3a14db94fe0b59ab6120a6 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 3aa9d513bb90d1e82d97033e0c11ab4537f5917c..30c9cc61c034cd292e073f5164d9308f4f312299 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/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 0000000000000000000000000000000000000000..93f922e6d08c77e576d4b520130be9453093cc01 --- /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/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 0000000000000000000000000000000000000000..bac0785b8cbe1776275d2c0ccbb9ed703052b142 --- /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/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 0000000000000000000000000000000000000000..870e7eab317144dbe1403a4b91a79513536f99d0 --- /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/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 4998bcfabac4afb5a3760c1359e1894430b3aaba..508f91d3f8d5d909cdeb8662a4fbd2cea778fc90 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 2a3fe7ab858abc680f75b5682a17e7da6b2573ec..1a5cf8b884ba18cfe4810234c88d0c1e0238d3d7 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 603dbd6cc5e555d8201212fb2b0f0fbc80532080..a645d605888b6da5bd2fa6a89c03d4054e7ef518 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 5b1200a09b5adb9149160ef4f7b7b90839d8cc4c..a460408c19c2644e24a0abda7138329128f78a32 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 new file mode 100644 index 0000000000000000000000000000000000000000..a581540c04a2bd943f1ac59bca6b8f226d12d884 --- /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/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..6f69a58a66a04fd0276bb2436125ca926cef4e8d --- /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-20161215.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161215.patch new file mode 100644 index 0000000000000000000000000000000000000000..3b81ad49a1e4f9f648704f18124bea4de820473f --- /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; 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 0000000000000000000000000000000000000000..67ff28d57aa9c20317de8a47bbdd35fa4585ae6a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -0,0 +1,176 @@ +# 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 ++++ 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/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 63e63419b2c20eee5ec0c4d070d11687a29a1088..5eee841793178fffe9de1f127ba41f6e4351a7ba 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=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb index 6355e7d5d7130a05f7e5efb81ce96f824ad04a29..6e30f9da8c564f55183427b52b738a5dfea1509d 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb @@ -32,7 +32,7 @@ dependencies = [ ] configopts = '--with-expat=$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=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2c01232d3e77ab4adbf785c112185cd1cd6d022 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +patches = ['GDAL-%(version)s_fix-vrtsources.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$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' + +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 0000000000000000000000000000000000000000..238de86030a90f6702e5e99afb0fc4100b532930 --- /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() */ 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 0000000000000000000000000000000000000000..bc2162b8fb0dc0069b58d9318e86fd7a30a7800d --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-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': 'foss', '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=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..015f10d5954c49c3bc045f21013b9d4f4f32271a --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$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' 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 0000000000000000000000000000000000000000..07385fe881ae18e18ab83f30548cd42cb37f30d5 --- /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=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch new file mode 100644 index 0000000000000000000000000000000000000000..c70a9775311e0c4aae4e18b98b77d9a97176221e --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch @@ -0,0 +1,9 @@ +--- gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h.orig 2017-03-31 17:06:52.996122910 +0200 ++++ gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h 2017-03-31 17:07:06.356370202 +0200 +@@ -34,4 +34,6 @@ + + jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode); + ++#define uchar unsigned char ++ + #endif diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..f10761fccdff781af113388d9472f6f9fd6dee1a --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.2.0'), + ('Python', '2.7.12'), +] + +configopts = '--with-system-zlib --with-python=$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/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 009df93cd714adaefba937bf406efc33c949d30e..b7ffec63fedcaaa7f369e1f5f0d64b94776a6848 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/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 3053b75ee06b7b746731a5b69a05cc53285ae92a..acdde9dd040d43ea2e1eaecef91dc8cd0afb1bcb 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/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 0000000000000000000000000000000000000000..02e7eb0e4003fa8237155738ae36352906d01580 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-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': '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' 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 0000000000000000000000000000000000000000..9997517749a76c7d88bbf532591cd68d73662fc7 --- /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/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 0000000000000000000000000000000000000000..4483d7a5d06335ee86c219e9dccc297acc10a872 --- /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/g/GETORB/GETORB-2.3.2-intel-2017a.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f01c7d156494c3b7161f58c51e62c4a63fe9e5d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb @@ -0,0 +1,26 @@ +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': '2017a'} + +source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] +sources = ['getorb_%(version)s.tar.gz'] + +skipsteps = ['configure'] + +parallel = 1 + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/lodr', 'bin/mdate'], + 'dirs': [], +} + +moduleclass = 'tools' 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 0000000000000000000000000000000000000000..8d11408e6b409d925cbc491e07f80055bf25aea2 --- /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 0000000000000000000000000000000000000000..3b289b47ea9914a160adf65a4256f4d77c03f718 --- /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 0000000000000000000000000000000000000000..23ba52ac639a32137ba2115450fa67bc648d3e64 --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -0,0 +1,18 @@ +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 ++++ 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} ${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} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas + + docu: doc/gfold.pod + pod2man doc/gfold.pod > doc/gfold.man 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 0000000000000000000000000000000000000000..284174920189e2097ab2e6368c5359c408df1e97 --- /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', '1.6.24'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' 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 73ce1be6d6188f150635c1a057c5e6487afda0aa..02f569f33b65a3fb41662b7489ec26d79eb937d1 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 --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 918c5aec064dd5b33c8bc696eaecc1e206361584..08fc1645190e639298ef62075c54c0038e07987d 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 --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 3e8dd8b2dfa13acd6e43ae320f2a4b53369f24d2..8ed215628abdc674ab8665df446d002bed8f257a 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 --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 cabfe78d325876f0484af882c23960b55c41cdef..0cfae7ee910e20ac7a17b8929a01cd16d09856b4 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 --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-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b20efcba16aa634a2e1919146c736de133a521f --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -0,0 +1,35 @@ +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'), + ('util-linux', '2.29.2'), +] + +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/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 5fbe4acc9a092714ef3853f276b5670b3f05ad5e..d00a71f2d8bd425c7a78138b2de9d2b798288e7c 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 6189b95fa0b2c47ae7ef7d7e9d4bdc46675567f0..3994be6bc47fdc448ebce007c7beb0faf83329a1 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 db19b2803a4505002dcf44d44ea5804488b30923..abea13b1cef365362c8817677513450902960d8e 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" @@ -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 84e054bf9ccf013654498c831bab82886f14a657..f2525337c6c64abecb776d96f5330f93e771125a 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' @@ -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 a8ca27958e85ffec8898897a2a72482c79457f0f..6b8d559ccc265ffb588a12db8d650a0767e1c348 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' @@ -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/GMP/GMP-6.0.0a-foss-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb index ab0d6b9ba8c8c678ef864cb1f99547ef59265dc1..e822e11f3565486ad8bf60722c75006ecd84221e 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/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 0000000000000000000000000000000000000000..2d442cdea2b611e30c4c3c31d204c093e736cbf9 --- /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/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 0000000000000000000000000000000000000000..046f2d17183bfac39e6089fc357ba7b8cf4c9c95 --- /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/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 0000000000000000000000000000000000000000..8f949a1a92f65346b64984ac6f31355a27a2f50e --- /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' 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 0000000000000000000000000000000000000000..76281fb06e1184a29f321c5292e82624daeee18a --- /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/GP2C/GP2C-0.0.9pl5-foss-2016a.eb b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb index e78f2ba765ca13f54160f88355d201e8564fec05..238da5f7656941d85215c25f62b660499da862c3 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. """ @@ -17,12 +17,12 @@ dependencies = [ ('PARI-GP', '2.7.6'), ] -configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' +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/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ad8f765c7535c301873de1566a7b3ee1eac5c76 --- /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', '3.7.2'), +] + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..c3f26a2915cb80eaf880785f60d6225ef9aa8d9f --- /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' 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 0000000000000000000000000000000000000000..edcd456df0402fbf1c8be4e5547b12548311fb81 --- /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' 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 7fae7e2b3ff44714c71a681f1b90bfd8263ee240..adf36de39874e48c24e0568e79667b9750cff661 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:${EBROOTFFTW}/include && " dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb index 83b2732fb5a3c0509fdce3a3fb7e147696885b2b..f52ab6e342b9da927bde3c1efaf6cc6d4a9b7fea 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb index 350a3d6cfac172ec6e9c4867fa56480d697124d1..3f046b21296946a718cbfbd1094ec16cbbd7a9f6 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$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 f8d1e53e321d52ef5e4afce53990049bf834ff15..5f20cd92b4bf2c8c85c81b760153cf55f5205013 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/GSL/GSL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb index 378ea5f63e4b90d37463e1638d2f31f3bd42c885..634f2c0cf81aa8c3d59980db1d7d346109c84483 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/GSL/GSL-2.3-foss-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..66df054b65dca214aa50dfcae87d1b1aa0efa2af --- /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/GSL/GSL-2.3-intel-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..40738004baec7b6b846e429bcdfe81bd338df50a --- /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/g/GSL/GSL-2.3-intel-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..23a2fed6dc0dbd76c2de90dd47fbddd886022ff1 --- /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' 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 0000000000000000000000000000000000000000..c33f283106b1e0ec6901a694c8a2d474845c30af --- /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/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 0000000000000000000000000000000000000000..a04d05981699baa2098592af2aac73e37e61b198 --- /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/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 0000000000000000000000000000000000000000..4e408b39dd8f6f54baf04257485b5b9932a95611 --- /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 0000000000000000000000000000000000000000..4327a994ef732788120ca67e9bb0bb9876f838d0 --- /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"; + } + } + 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 0000000000000000000000000000000000000000..0ffa31b3f440167c5c1ab8a6543f36c806419f29 --- /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/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb index 8aa2e7719b61ee95d7b31d1e873d886e9e19b754..0e4a638848e859eb9924b2da3f8dc04829024e7d 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 @@ -10,9 +10,11 @@ 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] +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 97a129a9e5a916b3842f3c9026c22a6228c29d2d..9bdfb72977dfc923b333a14f7fbfe97f9ffa222d 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.14-intel-2014b.eb @@ -10,9 +10,11 @@ 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] +checksums = ['586494befb443363338c1b6379f13973'] + dependencies = [ ('freetype', '2.5.3'), ('fontconfig', '2.11.1'), 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 4e828aad873bfcebdb73eca5e146e2cf372fc006..16ce3919c6cd8b500891136e414eb4a632d19e11 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 691a90006b03337bbf9d6ec36b65ee8166d8125b..16b62cc65deade066ce8c0b03530bac66706ae07 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'] 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 fa06ee75b25c99b265923e79bc398a209a33065c..9a3a3ea5482f4bb9b4960286ed0ee030731b2404 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/" + 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 8612f2848b8bc1e62a5dc53b6ea654e2da393205..0d5843bdd649f8684eb017005530770fa9a8eaaf 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/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ 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 0000000000000000000000000000000000000000..d7b08e9fef71d8098dc0bfe64ceaf01ad484539c --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -0,0 +1,34 @@ +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/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index 2238d98b96030c1f2bb7e28875c2c22d5c800f76..eed125d9f62af33f32727d34b50b531b2b8a377e 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 = [ @@ -24,6 +26,9 @@ 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' 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 0000000000000000000000000000000000000000..e055f488f12384755d1929a931cdd014b8a78fac --- /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/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 80b639f6e354f9faec6c75790063b782511e621b..72a8492f83d1527094178891480135544dca0741 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/g/Go/Go-1.8.1.eb b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..07ab4f25c48231aaef6b3e3c3b260f3a24ad5696 --- /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' 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 0000000000000000000000000000000000000000..ef9c393d1a7e6166cb816da3dbb7bd812dc41886 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -0,0 +1,62 @@ +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'), +] + +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/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb index 43c5a459fa807e35f8443d9da8a131b90d28c211..af08c394ee4b863edc1c38f8a7a2fa1feb888bac 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/GroIMP/GroIMP-1.5.eb b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..aff38f5ddf3a86b3988ae366eedcb36c29c8d20f --- /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'), +] + +builddependencies = [('ant', '1.10.0', '-Java-%(javaver)s')] + +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' 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 0000000000000000000000000000000000000000..dce576ef30aa2a98ebba2c45c3fc65205807a5d7 --- /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/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 0000000000000000000000000000000000000000..318524cbae575b04787ccaef6ebb998b332c62b6 --- /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/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 0000000000000000000000000000000000000000..91bbbfa89b16d51c1a28aedafa58095b0897e823 --- /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 0000000000000000000000000000000000000000..c7f92d0e2b673e625e9a759615b7083e0ca06dc6 --- /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' 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 b799146d375484f2b879971e91c07cf0418ce015..f4f2214acc709fcaf5abac1d8dd1c2c1de85cf2b 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/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 991e6da6fa638df04d53a8dd92704859848cfbe1..fe0e24229f49f1070690eb8969c0cdbfb2c49af8 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/gettext/gettext-0.18.2-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb index e7d30bfac735bde0a37a1e05bc5868106eb62311..400996e08a947c8dd74c9e14a780ef0ca0df293f 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 686c6f9d409515f4cceffaf28b7836983f8e6052..645bdc29becb29b383a945995af68a25750fc05b 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 adf041c9d3eb2dcd74c06c6fb8097635c548b2c0..ccaa5c1d29321d468eeff2b273164881b8740f23 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 5479e98f2377785512ebc77c841e63d362f8fb97..b9f046449caa0902ebe0c825cb1f1945b16d98ad 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 21f6d06397a6a717de016b55dba11adb76761c40..54b916db8ebbb3ae133d06b10e465f0a8c35c83c 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 68b4d25ce93c13c77ac16c7e2d6e7ec7fb960f81..000ef4aa2d927bc617a7024a0365753e35068550 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 a1a642076c1cec1603448da4b00994234d4a2620..eeeccb35d40f0917d9a3b79de16ba12a28555df9 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 b9b28dda44512de1295192445b2a890d43073bb4..827716cf971356a32f7dcf1beaa1645eac8edc40 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 238843b2065100579acf3cd7e19c1d8bea53a8a2..450a973ebb70d1f01413575a8443ceaff3c48730 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 a0c6e923392a125f5138c4f5f30352f46ea4298a..43c9195057d098c6c29ac49c122af7a41c1bbc42 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 c49302820d355f68de88379261ed6593732c3bde..57381cdd38f4d12a223c66867cd09bf0cb5492fe 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 2d3d1e0547f25775e4a78c691d7763ee9c2cfaaa..1a7da104405b3a83259e1adfe1c7af4e7fa694b0 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 7e8ff4e184d79e85cfff1bcbecdddb813548ef1f..27ab692a932d1855d78264750435b67266180cb9 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 51c244d3eff5c7d5b62da4103211813b817abde1..e435d001027d0d643f046b4b91bdb7246c9f1338 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 0dbf6fce3a8884073753360e0c6aab83b9d26e95..246fbea3c666ee24f0803bdea80ed9c8ce9d0428 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 ed81b95755a6bd661789a3d4b8c9c1677cf5cac1..11ed30961cdc96b2c87ed9e795e7a82aa8659873 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 90c8e2d47d90b1b8b50d39f83126af2a5477a399..4ff92c775ddd49836673aad6eb02fd3d456c0251 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 1fdb744032d4d3a52c2a22305425cb19a69b2a27..ac6519ed4adfa37fb522f77c3c71e2de9700521d 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 4aed92d350e6c1ccc8f7f2248deb7c3cb1578cca..859ba0f08fb2294e2ea75fcff98eb780a69ed45c 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 a9b8c4c455a989ca2e3e874136670178a912a7a6..802790cb291b29087a19bac4b663a66f198429cb 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 d58aad19704156cd425a3c24894c1991bfd0c3b6..220b284a16547a9c2e575b19348246a0cf04a1b4 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 ce355420b29f29b3cfcfc413c7426256fcaea34d..902bd2a2360c13a1e44695074604868114c979bc 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 690872c686f14da3d5a18923ded8d5ea5130107e..79d7c0db221d1036a1246dbcd7c2eeaa06b3382f 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 4580e48c6a96e10cf91935dae20beb9a837e0453..a61ec3269bf12a2aa4747de8c9ebd365508054d2 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 4f86721ed0a6a07d39b8f9363a715522f20a4c2f..57cdaad01b534c6a086157a8f9c7560c821259fe 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 578b07b38d3251d0eb20e2cfa52bd80ec2fe0a1f..8e1eda7fc94ec8c33839493770249c6b1d91d6cc 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 8e1b03ad2a1a31dd1f68eecf691a1562e36b520e..13b1f6601b02893e768c92d064212d6b4891c6c5 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 47b250264e4c3f0317e6231c0347043a8fac0904..8f8b64bb6fbb85be2954ed2710deaf689e1496d6 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 91c8cacd60b8189ac10043664b35c5137601c5ac..bcee20f66ba7707bb357236a504da7fba1327e9b 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 6df1b22caa7b36e881f6f692bac1571f6f8b0c35..8671de264d667929c382928a9116a40cba534c3c 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-0.19.8.1-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 0000000000000000000000000000000000000000..c366761771f4d26c62e835a6b1a2cd760a9b814a --- /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 0000000000000000000000000000000000000000..ee5718ec1115957204973f7a938d4a92ca1c457e --- /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/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb index 45caa1fde85d1e18b31d28b2386916b21e0fb853..dd9bbb81e0b8374c54586ef6ff41b2241287c6d4 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""" 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 bd4f6deeb967128c87d1b801cf8fbfb288c47bf4..c16d2b51eb658961f858a6f5b92c701024af684a 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/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 bba320bc05dc3ec301ff2d435cadbdf197c1af3c..7f241b68843566a53bec3a370f4f6380a77b7f21 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 +21,12 @@ 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'] + +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 4c4de493037651fe3ccdbb025998f1537947df5f..316219216f8ea8ad138c0fbeb79e36a14ffbffee 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 +21,12 @@ 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'] + +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 a705caba430736331b164e3892f49fbc5286d558..12ddedc547d70d0ff689bcfdd64b583d32f02e25 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 +22,12 @@ 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'] + +checksums = ['f44e7c6c689f58d1876634aafe9fe1f9'] + +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 6dfc4c5947fe5beefccec2a9479a1ab6238ddcfb..343da7e2bc5925c454b8fafbb584af9952b1308a 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 +21,12 @@ 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'] + +checksums = ['099c655ce47361850fa07252497f64e7'] + +preconfigopts = "make configure && " dependencies = [ ('cURL', '7.29.0'), 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 0000000000000000000000000000000000000000..47085658499ae7db0454d332798bf4110091e6e2 --- /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' 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 0000000000000000000000000000000000000000..20416b1946aac584249b1626d2311d7cfeed2f61 --- /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', '1.6.24'), + ('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' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb index 5eca4152c8a45e53da71501d0f648b277ce85fdf..eec2b277ee8aa61e6ccd06c7fffdfe078497c464 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/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb index b4350de73ad72da9ac3456b0a0226cc696bca269..7e7b36e603093c0740407afa626100348a9849c0 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/gompi/gompi-2017a.eb b/easybuild/easyconfigs/g/gompi/gompi-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7022e6111efb70aca680f95f3e53aedab40dfc1b --- /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/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 0000000000000000000000000000000000000000..51ca2d0db03f107bee9dc0160758435ae6d91f83 --- /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' 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 0000000000000000000000000000000000000000..95b77139aff9460b09b6e6bed45deccbeb8849cd --- /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' 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 fc1bd333582b8358ca3b4a69fec32c378097e1e4..1bf0222ad3e304f128dc125a87591810be3cd9b3 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/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 0000000000000000000000000000000000000000..7290bfdd17eeed831ac5401021b2f7009e2d7544 --- /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/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb index 3ebc1003fc1fcd76ba7bd99add4536cac3b5e5c4..0d6323dcef099cb3ce90fa61173abfd7d60156c5 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/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index a0f2ba3078e85e4a60fa1fa04afa23d2e2ea8946..8dc32d3aadcc4001ce606afbc26cf001e53b6129 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'], } diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb index ab9d5fd44fb20ffb2896ba03057ef693d7164e56..84ff25e5342c2454d7f75d7c9c15b6b36729c664 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')] 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 28e5e6ad3626ad60b49496476b9887f442feb4cd..e115932f8eef33e18f10fb021e9b965edb2db574 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-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..36b03f1853631b650b289bcb777cc1d9a83a1778 --- /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=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index fa2a08d015f88a23d2d45730b000606a4e9d4f28..16556a59b796f023c8128f302b0cc2490981e4a9 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.8' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..a728a33f564cad96ddd8a3dffdfc7dbc1e7563fe --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/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 0000000000000000000000000000000000000000..bc132a214419692c850a61cbe56b10d3688b5d27 --- /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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index 84580d9ba86a137adc09e2eeb6ca968d413db2b9..7250d32fe55abcb532b1aa74b23cd40422e11210 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -21,6 +21,7 @@ buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), + ('libxml2', '2.9.3') ] moduleclass = 'data' 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 0000000000000000000000000000000000000000..570e4a8ff2c0d568323e1f7188b7f4feec59fbeb --- /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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a0d6f2ef276a8af17687b684cdf9cd82cbd01d02 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.5' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +patches = ['HISAT2-%(version)s_intel-fixes.patch'] + +checksums = ['b6d867e1f8463012d1de3d1472573906'] + +dependencies = [ + ('NGS', '1.3.0'), + ('ncbi-vdb', '2.8.2'), +] + +buildopts = 'CC="$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/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 0000000000000000000000000000000000000000..571fc956b3fa2681524b1a9e11da8bc84dd63b92 --- /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 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 0456b6d6ce73de3d5b8884605d4437d1ca9d8fe6..aed3e32ba8e8b3701eca00d27e534eb8a7b54caf 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 +28,16 @@ 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"]], - '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'], } -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 da1af277a57ae99f72e434ba381340650a9cfb5f..66c915507d8d3f3a869893315f5ad4221f670294 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 +28,16 @@ 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"]], - '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'], } -runtest = 'check' - moduleclass = 'bio' 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 0000000000000000000000000000000000000000..3ca7456fc5db3dc48f57848f24360f04b022a4e6 --- /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' 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 76836f3aed65f5ef74804c5ac6a5e1dd427263de..259d3f70b6fb79cd254a88b100919dbdb7b102c0 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 576cc9a69949f30bbb82ee4bdad34a36f7e084f8..5feb085a7998b59cdd7789da3c481f3bc0ee7a7e 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 cf3bd5fd414d876bd49234ac60d05a98f1ddd803..0715af27f9e613cbb3fe25cc9d54985799b28c88 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 d327bfbbab7013ccee166bd90ec9adf6eac5309b..cd888a1b77e81fcd68e24512ef128c11a3f5e623 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 fa3e730343edb8f3debbe599891e7594e0821d03..96f1d5781af0b09a07f9765e3fad3450ae225e33 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 91a1cadef93ee07cec5acbf673e3776925b77195..e3f05fd328d56145e37bf64fd2038690910d35e5 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 934cc8d3eba6ae6200d69b2ef55398b3975cb5f8..4edf03da451c087bbc0ad68e4822d75da1442b3a 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 7a8e5a0800a1066a62c4d21c3218e1ef6c225782..76ee40d6521ce2fb91b13cac03275e13624c0bd7 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 4f4dbfc813e7bb2c067516570a5e6a6b23b7002c..2c9f0ea5ba7fd216596757dea9f5009a33896ffe 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 455f495e6effbee37ed41d4de3bd31a548ab2196..bff436a5d6cd66c84dce6bfb59cb70cf1fa5933d 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 f64bec348b182077ae3001f5fb4b62469e7948e9..b1fe7ccd3c8f82c55d98dc1c05be9832dc698e58 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 57414cfc792fc92cea28fd419453ef5940ff7224..c7a116c4f3193c87a75a01c820b1e26cfc74f3a3 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 b59f7317b17bb77c3fa73136961c83166c38abaa..b9880180b4b54364d2866f5087676be174739d21 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 00ee4facc9deb07e6e72a87f7a53cdfe19e45f36..4749294d9fc25edd6f7eb68c1eebf38a3a292092 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 651ae824ba838e35c74049fb2a3e6ef2a1b29fa0..32ea90665eb6798750f32aa91c44812908088499 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 9ab9de3734e6be345f482b6899caad7b8922ea02..ab2e745599d1097d3b0aa39e94e430dc4066d8cd 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 6e7b16eb218b302a6066f2eab752b6be2c3b27d1..c750f970fb68c0f0f26351c5670e26bf60e32e1a 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 225cb3be6afaecf674911b582df7b19440ab5170..97e132a043c1220913dd62345cad6793d907c0ba 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 728ad9cf2ed2e878b157a4c9277d0696b734a900..fe7bda0c238bed98d52a1bc7ad56df4eb3046d5f 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 e65fa73edae405813768602c29b28c43f3f096b5..6c486063ce8406667d3dc14a7265d63f81c9f032 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 e44a4ac54d1f94d5060c6251d9a82bd7f814b77f..416d5bc913dc35ef3cd4c802440dec9a649442e4 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 e43e4270ddec3ee1d1dbd17f9618c578aef2610d..df93eaf60fb02bd3bccaad0417e62e1a42168a38 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 5634e6bd4f5e7509ba9e568154071c1195c27ea4..c40112704f0853bf3a38ffe5c5b0a774a4d7bf4f 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 50fef4fac6d2cc7dfab8db6d121751fc72e08a53..5d0475520c01dcbc7014935d3d9f8da7264c669f 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 ae8a971cbf82e4e5053e35466e3bbdde03f12219..7513b5c69c94ff36fa06fac2eaa76976243cc608 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 dda08f35b905cccad0d20f13705724c590488238..7a3660c3cf1dab54254bd42e7c26f766003e86b0 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 d581afc6f7e9572c10e24cb327bcbc8c4a82c106..b99e6ef61e4236e0482acdfdc75171834696e797 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 fd109a8fed784e12f63123c33bcea17e86e0bec7..51de7973858027a1956a2f13795e1a39c91877bf 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 92f6036e1cd824ff35a102d80b2bb7a1494ad9e7..036b47fd973552452c1627d828b9aadd8d732d4e 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 55ab924d7d736c777533b724e480ba84428cbd6a..7fd7fc7bf83ad70dfcea29c5d85d77e9a4547ae0 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 38c3e337e3c2d694f19b28444f9e4692600440f8..595430c600376345dcae3754b99b0ca43d647e16 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 4c3646267b9389f92cded910602f7ebae3d22d3c..095ac318fe9b8fb622eb55f83beb3ab54e2cdb51 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 4e8b4379819c8c4691c8dda217812831dcd6054b..271e44e3ae30a54b4ed657bb8864dace20fb309c 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 07ff11637e2920a58d1c05743d8e32f7b7287786..1740a95776da82ad2290c4cc784f2cb1b44f96b5 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 7597cf43f89395fedfbd6145001f20a52d55db3d..bfca06cd246dd68cb7cd9479cee99045a5781954 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 4e727e3fcd666e95bd283da0ed2bb84b3fbc88fd..0be6dec3cfe3aba7709a9fb9e6787f8ffc39bc33 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 97b6ceedd37022a3fa7cab20ebd576009f904a4f..774ed3383d9b64c75f1f39a1ada476c6a46f157a 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 fa34ec665e54f173d1b536839ea64eeed157db7f..ecdaa77a80bc51227f04c8c6e6a4a021d8b39289 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 406d3ae0390e2b0c5a289ccbc37e34796021dc48..3f8d9be6d0d9d3b9418540b08a54306db9334ddc 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 27b235374a8e53222fce30b1901e511e71cf16c7..7fa2f2899032ee52e51bfd360a992ac457ff3563 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 977c7d487d17b2770aec1bfd1f5449799864b0b8..21af879c00d447ab67793439eca0b6d12ff5c57f 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 ffa453cdb4c22027945f80f38f679b2b266c405d..d6bd01277c29430811ad42c72d242d9ef5cb41fb 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 f2d54cf6714852cf5f4d1e7ee498b5082a1a612a..2c8b3ccfcc2bee1aa1c431451fc2daa9701b81cb 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 7eaca67c162c11e2ba28214466a4f616ff575c9b..eb86100453503cbfbb654bd9462206296f4393e4 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 660c68898c6491851ec7de24000f66d3ebecb556..3aa6c8de88010341b94d63a328c35808d402e1bf 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 a3af786ca9b1ffb63b6a7bafdf7fa91941026405..2349780aefb94f352e3f524196c216e72d262f83 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 226f45477c78828844d9f938969a2395d1a7f362..f4cc3988331c439b0420e6073df568231b9f688e 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 e2c8df3cc68517ddbc2ac4509234ff85bfd786ce..8cc92060d31b388b2cd3616d4473732762317ca0 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 28511646d6c395e235989d3cd47f93e7f9c45552..645f1e333c499b5498f5cdef0989c2262cd41c51 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 59e1705669a58e507e3b0c07a4f9a3230047d081..2247657f83be34460515ff37c2d2c1ad00b59063 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 42249afb29b07367e46ba3664145aa64157146b4..ac09c4d824f94017019c040ac450c7f5cf60f481 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 9552b4d6538310a00355f603dd608df9a95ed9fc..2f6f29630a1077d9fad018d0d87df46cfa776ee9 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 4d48990b54201f49d2431bf8708ced105e36212d..9b006fcd88b0185a40fa72431b67a06190e2a342 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 112d6aa6345556e239cb730d1c4073806e3eaa9f..23e9cfc7a89be5b72d7a2702dffa4920e8c1884f 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 c44018425b1dbf270179e425446855c4505a5065..09db01519259e3201ae319aa37ea4fac81843470 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 be4db4593ebbf63dbc96873a396af3027feb9a97..0766c108873a2ef2d20befb2275e876d8a609d1c 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 new file mode 100644 index 0000000000000000000000000000000000000000..95e36ebf9580ecda9825e7236b7a43df12f6bc1a --- /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/HPL/HPL-2.2-goolfc-2016.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb index d1430d0e3a6cc7780a53459c1cc9876dca5fe4da..c13e143bbf81d8f120b04a51455d06218207856c 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 fff961832d9eb1f2bd5d0454e15202579d40fb56..069cc730f1f6150bc50f1e31f9406a2ea89518fa 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 48447ddb2875e9466b5abb785b368f313cd8781b..d09d150a574e128d71b0bf3fe396bdf7351ee239 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 64700f3b27967a0a985c9d2e5a91f970cb3ee3f6..0db9bffabb1779fd850725591422a52d13d45e6e 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 new file mode 100644 index 0000000000000000000000000000000000000000..f53793fe5b54e38b442ee4a27937e396cab60dfa --- /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/h/HPL/HPL-2.2-intel-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6caac9093010bd7c077d446989acd4ee7bf589fc --- /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/h/HPL/HPL-2.2-intelcuda-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb index 05f316bde4de14d79681c71a46aa7e516f2bae68..b6258c055e0871b2930d3cde148b0be84ad6b653 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 22cd32989a753684726798def06fc6c15b6b3f24..579a2931427736ce6cad3954230fcf350a767016 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 efda5a282ce5a5f4aa3691d405ea905127397b4a..ed855cdf2a2d4d63aa74004029c6c9ba32d4fbdf 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 d890354a7b87adf022e459e30c45d8348dae4f5a..37c0a37f5d428c5d7aa354c52515c29693e68830 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 new file mode 100644 index 0000000000000000000000000000000000000000..77467edaf2843a4d0778080006ae7e77fcb770b8 --- /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' 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 005a57564c099d9d6127e09c08dd53386f3ab522..3ef2663a61344d67e9f1740602138e7e665b7d05 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/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 0000000000000000000000000000000000000000..a58dae978a4c05e78fc187fc4f9982b81159f1cb --- /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.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..9bdb215d4c5d73d4113385fe4062d8880bb624d7 --- /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 0000000000000000000000000000000000000000..5c5a91710c7538773dbf9d7655cb650b8791cc29 --- /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' 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 0000000000000000000000000000000000000000..28916e2a3a177c408cdeff2fd0b6319348e89c80 --- /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/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 d46bdf73671d606a14163ce92c3830d6806a7a0d..3b8e3663007b6917ee82fdf28312ea83dd19e49b 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 44e47d185bd9228687d22902455a1720cd6014cd..c2eb89d992465f4d791cca1aa2cc72deb7c892bf 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 783b534519d5f33ac68f69b77528765c9a6354b8..f62ed07a47f967e1fa265edf64b7eb35345c72bb 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 8b0afc7b1f5b7f0bd19946111382bf1df8603d53..cf92cc3c69211c7c9b5889279271549d0c2adc64 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 80e0503ba7c1e8356b383b5cfb5341acada999e6..5ab80c6f39c569a35f7b855f9429b18f76e2ff9f 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 17626346c54fc2cbb99db108a062a215ffcd96c2..72344ad38bf27b7fa98753a6fe186232defbe085 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} @@ -15,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ @@ -26,7 +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 12d6705dfac95ef61ec59f529f9a3e3e14052470..56c251d6fa8aee73fe0ab4707d52e7593368d92c 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=$EBROOTHDF5 && ' @@ -29,8 +28,8 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], - 'dirs': [], + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..adc15ffb81843e9d05189acb5e047dead832e855 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$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' 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 0000000000000000000000000000000000000000..300f1e3d6ee9cb341f9a4fb7762b81a353e0f258 --- /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/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 09424f6b1b6c5faa243e38c8292a11c17e900f9f..b789858736594bd6e9ce02e0697313fd9977942d 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/hanythingondemand/hanythingondemand-3.0.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb index 3c591a65e9be2e3198b06c4cc8c959b57538875b..f18772cba05ef042012f34062ef03d435e0298b0 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 c6c633599b5f02d1da7b136cabb29be218471f10..7d698aa331cf23787c9a73c98ce5769c02f8d81c 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 a6a417a8dc04bf875d89c414c190f062222c5450..79d83ae2496bc69ba3545bc57b1275b62d9cceae 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 996a654cea4e2c67d8b1affb4916bc1222e405d2..be5a34157ba765eaadddcf12a7dad36e4f552ff3 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 754319d620b8688bcbe1fd8e7b4068a73624ecff..e614c725c01524cb5fce1c300a5917ba0ab3d0aa 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 2c68b1bfaa0490e9a9d7c771c7bdbff3cc0286bc..82c6cbe980c89b5be8a6bb870ab474fc62fa4cc5 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 3f8a48b472b4412387a3fa56efac409697f4bf4c..e91b71bb90e3f7d1c0d4bf86aae14d4de5f46215 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 cb9ae643329bb3d7e33e78f1d20cded6ff461a32..4862029e8193a4829fda7813f5603ab664617edf 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 4846e39a8eb054ca2f45c2cc67e241b8aef40de1..9e46040159f7eab7f6e2795ea78d19bc1bb1e596 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 275b2940c7532bcfce2f2ca03605138b03cd6e07..882a63bafc87765491d5cd1536d1f2eaeaad3aa6 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 7e255dbc21069de0b625f82f16495165f31314e6..da0110ba9dd9e6ccf5a384e7a8d94cca4775201e 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/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 0000000000000000000000000000000000000000..0d730043fba1ba63b01ae9e57ce9e016d6e66f3b --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.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': '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': [], +} + +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 0000000000000000000000000000000000000000..4931b9f6ce3de5a153e0f6fd6547b928559ba53f --- /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/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 0000000000000000000000000000000000000000..f487ba55300bad73c8c8f348ea7d47da9939efcd --- /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/h/help2man/help2man-1.47.4.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..292de661e9187905b8b401e66f3f854be490d8ed --- /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' 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 944bc27a5ec17eab134de543750e5ef3a3d0bbd2..4ab8e8fc9aad1c481741f640ba5a3dee42bb5fcf 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" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 778a209cabe0c147c85cf62c19ea29f6027b4c18..401ada28eaa083dd60fc833cfb8403d02974c3a6 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb index 3f0df333bf499fe295792152f0d71a54dc38d4e6..067d4ce4509943385773d43b8611a411a53b9750 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb index d1f6974e2a78b42372ffcea15604a3104109a6ea..786bdb4f54a26a1f6a10f738c69643d06efa96ec 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb index 35ced3699b49ed078f23acf88ef16609aca3680e..071326cd0d53773cdeb0eb61c8bb3a3ed2074a0e 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.4' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$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=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb index a83862d85314b3221ef2ad6b80eaf180672990b3..ed51d673262eca2cdea5173a0d94b05cfed6eda8 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.4' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'gcccuda', 'version': '2016.10'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$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=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..1aeec6a1167dbc2a8f3a40b352c5700a5358e5ed --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/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 0000000000000000000000000000000000000000..51bcdefbaf0231480cc1a71d2322710b8839ece7 --- /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=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000000000000000000000000000000000..93ceada29dd4444d361a44d7a6bbe5286a585034 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.6' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/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 0000000000000000000000000000000000000000..ba4de3d90675707898af5fa33dcd7b8912805008 --- /dev/null +++ b/easybuild/easyconfigs/h/hyperspy/hyperspy-1.1.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,71 @@ +easyblock = 'Bundle' + +name = 'hyperspy' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +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'} + +# 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' 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 88b4f2e32e2230407caf75d63ec139befe22c4fe..56a8573d697de73ebbcccd83e5d09a1f2d21d034 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 fccdce2d5063bd34b500d1cf9cd0fc2a84bc4598..66efa1aea5ca4986008173671f67bd5e9a0caf28 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/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 faccbfa2f16a5ec4601089e37631785770dbb3e5..110b4809235ada2d3ef2e8f2739ed86545740e59 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 444b68f2e7e024a0bc848f5d4a020a08b2e097a0..f8dd5d79f289a939241be02f85879eacf4e07c26 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/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index 09fb675534c8273b75415b919951cb4fee09aa31..2b74ec6d388777348b43fb7b2ffe6106c3bc337b 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -4,27 +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': '2016a'} +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="$MPICC"' parallel = 1 files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], - 'dirs': ['bin','doc'] + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': ['bin', 'doc'] } moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bcbb961f34c3dd578de7991cb7ac30a415a07d09 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +buildopts = 'all CC="$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' 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 0000000000000000000000000000000000000000..d22113b5a933dcf2e3b747e661705a9fa73f8603 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.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': '2017.02'} +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="$MPICC"' + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': ['bin', 'doc'] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6636a983cd82798b158b8e620cbf308ee4675a2c --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +buildopts = 'all CC="$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' diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb index 54799f31a3cc27426b22acdc41f4df4c3aba0ece..bfcfa298dc77052f43695293b2fc1b833c801d0a 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 28cdb8a360da0a5689161cfcdc12cdf25cc3c911..6621f7655d9bf1b49abc1c253475489270e74500 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/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb index 521eb6e805ea754a2aac71e9f2568a387f74cf46..66d029ece5c0cb8b50d4f7d151e6493dccf5a1b9 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 @@ -6,19 +6,19 @@ 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. """ -toolchain = {'name': 'foss', 'version': '2016a' } +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/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 8bd48f9c2e06260dbcebefdf859096ddea916dee..6af67462a39100f886d71e944f2b26953b5906f4 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'} @@ -19,17 +17,18 @@ 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']], - 'share/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/i/IPy/IPy-0.83.eb b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb new file mode 100644 index 0000000000000000000000000000000000000000..661784d022f7982582531fa9b9e02f2f5a5372aa --- /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/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 0000000000000000000000000000000000000000..ec7c04c10be1d797c21cbe1fc5998a76401b1738 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,151 @@ +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), + ('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/'], + }), + ('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/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 d3bbfe47b7c0bfcd1a26acaac76cee676caa0ccf..ad14e82e325684c732e1360b7c86b66daaab8491 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 new file mode 100644 index 0000000000000000000000000000000000000000..01c5f93a200be5360c9bf6dbd67f13a6e316e81a --- /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), + ('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/'], + }), + ('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/'], + }), + ('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/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 0000000000000000000000000000000000000000..62ef063309c112352815d3d717bf69bf3af34029 --- /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' 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 0000000000000000000000000000000000000000..6deccec5e63c1766f51240c58e5d53b3a8da7d36 --- /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 +-- 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 a303238f9baa35fbc99998108c12930223c78d20..6e5acb74b196d055c3ec7ae29b9957016449ee8b 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 e711a7699f943604f90fb879c2b6bee8ce487fb6..00012d332d8088d8f26d858f4846a25f1bbfae6e 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 5ae9fcabbc1acb996a8a8a62bfbe85039c8e214a..a5f0f5cc5f17569a06f21436beb592968a0ea109 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 bd7c2f7f2a1f70a91c4193c78c1e06b2a293c1ee..6fbb191c8bc2fc5956a34579c1e09463d078130b 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 6b38a91f39ee72a74dd68ba78fe266d1d76e9dbc..e6211fab28c58c4d34b8a2b6fce19d0b22ca7ab5 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 a7b67d3ddff0859a3692e29edaa33969091b3618..23ff5b76f64dda2dfefb3b5523b85812ffd2c0b4 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/ImageJ/ImageJ-1.51i.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb new file mode 100644 index 0000000000000000000000000000000000000000..8963988c6f533dad7df8b645282c78e5328d2c3a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.51i' + +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%(version_major)s%(version_minor)s-src.zip'] + +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' 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 0000000000000000000000000000000000000000..9875b136f1926ed0ac89f232b1958084ef5f64cb --- /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 $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGE/plugins'\n" + +moduleclass = 'tools' 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 bcbe21baac1e1abf56cfd3d58705c89a472999cb..9914e312e1452c037168f08d7ec544c9936e815a 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 cc86162edac40d38fd3608cb211b4818e2d8799f..ca7cdda8cd8a31edba5a1fe4286ba68644a5d679 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 7765318123ddad977e8952e269cfde8122919a33..346c8ee58bdf98c0abaebf1e3d0f012554bd8d36 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 d83125eb93ee3200df0fb25d34ffb690d8c3e89a..17c246342c9b601f49010dfbc4345e7b2b6904dd 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 f3c4211e8402f81d9ec9f85e50cdb6e19b97cc76..7e4fd1539e4147c1efc7b7071b9757f7f2030ca9 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/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 0000000000000000000000000000000000000000..b01509be3a621f7ee2e732d3158d250c626f9577 --- /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/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 59aa3e741492c6b9b1f44f67b2743d00a5d432eb..ab3458b6cb7ef6b38522159776546d195ccf72f2 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/Inspector/Inspector-2017_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e1233098f89791ab58b3c8819f6cb8b710e6225 --- /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' 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 0000000000000000000000000000000000000000..9ea21d95ae2c4ba6f9d0994869603c6a85e050a3 --- /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' 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 6966353326c301fb1382196161665d667cf7b8a4..5ec986a81715b82b05bbc895c3b04331998cf46f 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 4e88df40472d2e7b4eb64f1edc2f0f0848b3c8a3..06af631540b058001a6ee179a57cf6c3cfa8f0a7 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 a0ac2c0885e18b579609756bf050f20b90bc0439..6b3017a194a4d19eab72357d3615df6f0b15f1f3 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 efeb188af27eb851a0f7a33b1149ce3267a240f9..e0c5f7e40e73933e9be1886c1ca68dae0f130281 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 25d906e87f98fdcf49d97b7e33a47ef2792f1bdc..6db65c8a2e22cbe3910fa7f8848ca407be84c4b9 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 270e177a0c9897f3e8e9fb4aae5d472829994732..426c8d4726ea22516d361b0fa516b9890e42f73d 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 005adc34f3d0590251dc8b76e5785570cca356f2..367d02cc422253dcb22dc80f1fa7b9a56256f728 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 e8019bf5f8095675caee768630f69b0d7b063290..df976c997d0a73bac654f6aa500e50b1dd5fa2f1 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 17d0cd2bbe2f49b3802655eb53208b1878f25d3b..0e9f7290102feb4d9747906b024067b0b51f48fa 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 cf51e4e41b208e64d6b377e02837430741d295d5..69a166ec5699f1a481f0eb28b2ab5645706fb0a0 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 4079daa6ca034c4087e792e8ceefcf4309353256..5c240e5c11fed57639bb4b9c968afe232c0aac54 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 818ade63f27a074da6f85ccb749eecc8e8b60980..f259138a7ef52976ad3134f62185901d8a3fb270 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 086b7132e24044fe48700d1d38abdcc881cf907b..c13511557907f123e20a36dd3b9cee2a7383a604 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 08d349665671d8bf5397ac6550ec95451430f600..b9b8d9d6de47715e395175b806fa5a2d09839aee 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 8c5cfaeab570223f35902d4bea35b4ac94b858c0..db58351c1bbcaa6dbf872f24443375056fb6039f 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 446396ee03bca9646ad8dc1b95f4e1ecd10deb25..a1fab236a759fbb5005a4dd0dabe1c62a58c1118 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 3be64f6a79c4707ea5dea157bd24bfd174f7659c..e42dd9678eb8fa40de775902eff64eb10314894b 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 be5072e46d81cc37678c809b41a7160eb205772d..ace7d022386d36d5902c030809a2469b394d6701 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 2e5244fe910694eee77ed34c036a6841fe090f3f..b62448cecd9116f7845b322bcc1e2651677355b8 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 b742c2c7e4483b00d2a57d7b07b5e8e3b9d5f79b..939c07236347df5d211bb443167faf016e3e58f4 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 e4c5184bc06b21bbd24e8e0e6adffe77b75431a6..3ebed03a030cf5b98f6a66f007165eaa2350cf2e 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 5850a5593b8fa689aa19f82bb6218802df3e914d..26892de20b69bfea135eb8481853fc318345cc03 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 d02dca7d2281aaedc0546b3524d6173c5d37f562..e290c96aa603893d2cb02ff047408975dfce302f 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 dba6123fdbc2cdba87b15cd91840e812a3d7b1b9..352973960c4bc09946921d9286863611b018dadb 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 368b594177c120009bb61d4e425661a0b21dd4a1..13ebafc260640f9addfd1e53b4d5a59447728e82 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 08a67483318c06ed33c6b9a1a53646e7a47b7a9b..326875c30728d64fa098ffb3ed47ffb61fcacfe7 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 8439c044f45586a1956d414446ce6cdeaa1d896d..dbb4b840399886aa541bf68140f56b080cb36baa 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 37331a148806eae1f491109ae7e963dd503e9318..ae1d56e8a6a7a002e36fc545526119dcc06acd9f 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 55dec91be55769f4d5b613c34fd41901c312f15c..833da3c0c7edff4c883ae42ade96243d9891c152 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 1ca6568cb7049f00c1696a87484efb06caaf1028..b9a332e3a0f02a28b131a9cc6ded3385fa3018b9 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 32978c0fbefda3cf7eba628d0d7627109bce171e..f15a97cd309b34c52466435f604dff3b4f3dd59c 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 e56edba4dbd114128b90d96e06a41e1083cc9fe4..18895dbe61c12323d5f55640289c64be778b90c7 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 9d56289dfcdb4fe2dbbe093232f3f1d04cd4f600..d375c69cbb5c85118851693efd789a286c6d7920 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/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 0000000000000000000000000000000000000000..39745a0399f7615b9b1776f8d91c962cc833f6c2 --- /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?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' 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 0000000000000000000000000000000000000000..cd7f8184fe42e0fd59c20f18dab66d9df6bebfbd --- /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-2015.0.090.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb index 51b0376b09a253e359ff306ba04eb583664968eb..ebdf9f10ca53f797400484979e7a070c09d15065 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 cb21cd2b6c13b70b79aebcfb6bd6e46db650ce71..06b3d4cc945af31394a7a1515320e5269c82a853 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 8387432380faa1b66b676bf56a488f1a29294895..7029a01c14077d3f345d445d0ce458e380c7574f 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 f1a5e6d54b6b088a4a56662c8aa27cb9ac6fa84a..d51e11b54101e7a06dba334161c704515d6dbc34 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 a66481f29cf39a4d93f5c694196bf56cc8255ba4..f03bb37944e6b893b2e808e231ed29dd307c87f6 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 618d381f6ee35ac10fc0ca1dad9996c8f6e18274..8bf45db5e6db12497f2b3e1b3cbc05ebe79cd7a2 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 871fae395a716b77de72c776de28e2125b8f5f7d..7fc5fd1e8fe8ba51fae723549406836ff809f9ef 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 e07e4371a20e3d6d836330d7dfb2f21d088c286c..0b2036c9e01267ef9a44aec49f6733ab0533c924 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 73f4eda01fade1c0d4a9bb6629725bfe8f3a3483..f961d74a1f11c4392557469785e099db54fdc4b1 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 a1f40c75aed8a2894454f626f2b3588b032f4e82..f89991b41ee5196849f4ea56b1d8be8df149dc39 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 944d7a23b2fc72a2d39794af3a64e96db9b69648..52e91145c61f4cc874a32be7f6bc8ab0aea9d64f 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 3ed3f947b9c1e37ef1ba5888c177bb2babe2fb96..e2ed764a7b491dc64cba92b8b67b69b54eece03f 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 8034a2a1e14089ff5211cca11129875e8239d2e7..6e347be3a272efdff29850241bffa6c2016437dc 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 new file mode 100644 index 0000000000000000000000000000000000000000..ea60f74334b07c4a2619c2cc50346b39e575ccb7 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,19 @@ +# 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/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 0000000000000000000000000000000000000000..d622580adc03cb05d6009d9b9778df758b7c4417 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,19 @@ +# 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/iccifortcuda/iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb index 1eeb749c6e9c13c431085f724270ac234986473e..2e8347c1befb9ec877d551e1b304074efce47c19 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 ed01c4e7446195bd4845fce582e94f27d6e06bd1..ecd5b0b755e92ffe4cb0bf25c55ac831d315a93b 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 fc33afb1efbf811ccd24f958dee370f7bf65c241..7f60c5dadba78d8a4db75e4443f2edd7b9f43f18 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 a6b070f713840f0e4536fa3500c732eaaf3850b1..0cd535b843ca72619cd50da71fedcfa65fedeff6 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 aeb15217ff4ac85605f03e3346145025f26433c4..feae6d3047aa3a362066cddd2975b953f84529aa 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 55b4f558df19ab753f62486e0575e9c251d75abd..7d3a7fe1328d3ed61bffb4fc76957a242f007d68 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 e5194b8648c120263826ad4029dd100651d0d60c..72271c8f07c72087ffa7d6a6910f50c65e45c404 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 41d6ceb53e4a44e910350d3fe70c2474d2bca458..fca7778a457c96d096b458c4208eff7d046a3532 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 b3dda3d539270dcdccca71c7ba4ed845ad7a3a39..d54f7d57248e3a528bdb15e94062d01df446687e 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 6190ed29063cb5fa8e792ec610c143be93114617..e482585790cd55a665e44a8ddf889ba551e9e833 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 c4b7144887e9b37573e7b9e5120cab68c067715f..640705e6d02db8f38c9035a8bd2bca41120cbce9 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 da0e19e8a73155220b3d3a0a1362e9483be9a479..ee69dc8e336362d411a7fa66e83c578cebb74ed2 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 f8534d1717c79ab13d7ca099e7492e4ce272c97e..1372125c7ccb40a376c0cbba5a0a674d0e310150 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 c0ab005da23f241fc7feb5b92af6ebf85ca262a8..222eeaca4e329c01626f4136a58eaf61bb0d23ce 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 8d6eeaafb43bc54c69a37d838f450ecef92849b8..ef3f60866f222ee182908d33534fdefd57d0bd8e 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 65ff75aa5c642b7ee397fb4c8d66a404fb4c579f..5b0821682297ac6d5e769111e0357e4160cb8b74 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 0749ed0e0cd11c763ba8a52f0db412a7f83bc975..ad4923d07444047e22eb169511db5e72173a542c 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 99bf3863c6ded580bfa12f1838003c8af6b052df..43b7969dc4be0e5c39a130f21df6d6dd314c937f 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 54b49ddcaf29aae4f09d3b32908764e7b91f33f8..018ac9b87dbbf810bc7419664364cebb9a0386c9 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 4efd890d239884aa9bd743e2bfb7c3d81e8a5f6f..d84bb054d0f9226b55ec0f18f8a08f71d434298f 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 05c638d45107c3a9b328866e7a27c5d826536b4f..e1ae8632f175c2f971cb0312443a5e96855a5338 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 901fc019cc7f3ba3dc4097b62266d151ff9a4297..0b6f0c22abeb8fd1d1f8cb643eba2ee451191e0f 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 32705da10faefefa8c52efdcea411afe8b0d3606..7b9de4dea5ab6cb81ae36953f1b5b9ef47243877 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 dc69a4da5ee4b3e743be8fc40b3d84db6bb61a9c..6402e2f9aceb592f9418a9bd515a4e4e6b3e8ce1 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 8d50c3c4603c5345c9ae67a51489baab1b48540c..c762cdb26a3df6adfab367d8d6c8c0d964bca4b3 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 058b29e416d7420732e068fc6bfb2b6aca0629e8..f987a0ac44c199c0a1b9c4726c7aafd6f1d1f2fd 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 6a206056e1a69b3bc6f76c332d225e930a9987ca..a605451b28a1472797923342d5ddfaeb2f69492f 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 4e061aba7c0fdce3297312b90923f47b6d7234a5..104d8f27705ebc2b2af1d5ed7df4b986a7936189 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 a94df9884bd0363204bda12daba89bf92a9dd2cb..420984ed94576443bf511b7185e176d7b26ec4f5 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 62bde3a68e91f72bcaec8d9f8f998615892bd238..b312c804d8182d0ecdc3c9bba450d64d71341ca1 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 419e0257c0918bc09851082a152b1a35a3cf4cfb..a775af60a04e0f27617cb3317764423c82210570 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 02137b749816da4ac13ae45a65bc753fa349cac9..c2c4c3e7d1a137fde3d1de5201fa77060f5ceb84 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 5767d1400f2405ac64a1aa5fcc1520ec39404aa3..647803072820168c6d106ed7604651c712ee5293 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 0f54df3a82e9919122dd17cf8d1cdcc8a7c74f83..4a9762b2d0ea07c128dd9e3f99a037e1e62a85d0 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 8253a3390bf1b285389443b8f083d2d3d9c46fee..6e0324f9b50d77c410d5a00e83fad105f52450cd 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 2fd9b5a9467ab1b0bf0b4a2f56bbf539d2d3863a..446656fb7ad6d7d88aeb77a63f5c3c1730f01dec 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 9599d683487fc263f0e6d899ea6c977513b6ba29..a32fd8278aab33f6d38c04cd67fed509a43247aa 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 657a607db362a9a50db4d18b83f05958d563fc18..b40428eab79ccf06c682f0a146349e1905883281 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 9afeb8bcc99b8c6a5523c76af2fb6b32097b9c55..fdfcf853b676c7793726b07dcaf17667d90c98a1 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/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 0000000000000000000000000000000000000000..746cfd78bf9c71244df3fe0348f57efa870f405a --- /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?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' 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 0000000000000000000000000000000000000000..c4b671b6975410e3e902d66ea82504d58ec72d08 --- /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/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 0000000000000000000000000000000000000000..81b9d69187a5fa607dd1daf61ebd031fdc45662c --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch @@ -0,0 +1,49 @@ +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 +@@ -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-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0f9d10dbb15b768aa65039188778c0284770480 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -0,0 +1,34 @@ +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'] + +builddependencies = [('Autotools', '20150215')] + +patches = [ + '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'" +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 0000000000000000000000000000000000000000..339e68cee3a9d500ddbd7686d3d77717906bfe46 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch @@ -0,0 +1,264 @@ +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 +@@ -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): ]) 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 0000000000000000000000000000000000000000..b0f86b1096f9f52cfa96332dca82ffd9371cd01c --- /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/iimpi/iimpi-2017a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c272ff080320aa6c89cc578aaf2c67d9d4292e3e --- /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/iimpi/iimpi-7.1.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb index d62bc1e82f01fd184e814c2693ccb54e140a1254..8ea51a816a17cb6dea2ba77f935efc02dfe6a890 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 b0fe67cb26eafd431e86a5f22653622865fd9ad2..7f36db9539006e1e0c6d552da1876fceaa10b607 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/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 0000000000000000000000000000000000000000..399d48b06bde2f9319e6f9a7d69434108f5d42d9 --- /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' 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 39b3d7cf7b3c595141c73d338fa030958053b505..f12c8b0a4a47880da2be3112a296c7d80d4fd3b1 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 b1eb6ee6e39a4eb88b1bebf927538eb0614aa1c2..16e7150410f06c1b3955e03319b54dcf9d4a0dfb 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 91c64cfa0d5e70274c1d330775139846049a4c00..c3482af83f58b9b2d5c90457b0a43627c5095b1e 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 b8769ef805f7da0f9c00d64151c423d5b5d01b04..b9464f9703d06547a74acd38884310768aa350b8 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 b5b58cc1885370919e49fdb7da5a54164cf8788e..23c4595c4551246df7e6fff7d88336a35b5f1491 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 8adf971a63b6e0daa8529ac8eeab1d4ac589732d..11b669be478e2f2361452669630e0e2f27749d88 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 c1e7124884bf18064e218b2e73422ab2f763caf3..cf9de7a5fc5d3fa0379a8cb8cf810b7801051923 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 ccd95b2a7ac92e3db34fd79f9d813a4f47c88b27..beeabe2d9670ad07f4745c0def15aed4aaf3d668 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 74e9065d7ceb9ee34a9266cb843210515b4d7af6..36091633a7aed21d561fcead6781010c18632027 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 8b97b3ff265166f10c5fac0f5854499a4144c1d9..cfa4fa1e119399d3b38d197c1311f89a8188f381 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 471f7e9aa6330517fd062b3442eb6a021cdc7b65..ce891766f7cf1b4a2309a899ed4da8057a24cc47 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 98e5ffd25fb55b8a5289f64b0d79f61743c64c10..d8ef766bc11782e4d19c4df2948f407a0958b7ad 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 e04b1511363de673517ff592f95da214d23ca8a9..5c4db1885b7554d260db6edcb221ae0de653a56b 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 0d09ac1d4b2b422956853c09280ddb4c1b62d09d..dbddd3cc867f47bb312964de366bca865222a3c8 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 0fe1b14e46ecd70eecb2ac8446a47d8c0688d434..66e98d5997770c12adaf535e03ab62d6afe61be6 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 7b7f159547c27c6f4dba8d1e67410c708ddb1792..3c52f96be03b8d40ba0fa409399b0680ffea9928 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 e37a375b7a49e07166b205d543acff55e383412e..5ffe362a5899556d97b27f4fc6d23bf29a1078fb 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 cc9f1d89b5d1922fc0ab58e82a75f98c59dd4d5b..581df89fa96a3cb997b5508d0e3b1d29cde3645e 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 3b9cb14613ed640f57ef0823ffa3bb005afc27dc..1381ccc44ead27e58a0b457c867bade9171cb5b2 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 4843fd2442624f5d51bf92e118acbad744d00de2..b0b43aa3b00029b484c1344368bdf276ad7c3ea5 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 3ad520461af4c20ceb2643c59e868d02ce774cd7..7a0a1e53524079f42b5d7e189151e914b75319a3 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 2114374474a42fad3e1dc311dc92ad9a15fb6207..846edaec6cf7ccefe103b7057baad66ecff3be6e 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 8854a895987182eb6dc77f0968c617ec1ad2ec6c..82e9db5fed1990f222c3dac80b694b914d9119b4 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 2559891bccbeeb27624d5e7245613725bcaf95b1..6bbcefb5d7b60ba595d24d7dd3186b59d8674e74 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 47e59ba9fcd62671a8c558d951bed0558d1e4f9f..ddbbf90fd93f89b5d40a09823def12700a6fe4bd 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 bd599cfe0d4df98d14fa27f7b33de0e9871f276f..4b1c8e4141d37773b136ec7336721df213e33f5a 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 dcb2085bf3f7e6dd45ebcd6112a89716d3389d38..7028d56135c5a6b4144840d00ec8c3d25a279388 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 3ce046efac053e7b4eb37c6dfa51e8ac4dbe12c7..c0c59f157028b162b1b6306240801ae008a35796 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 a249ac518b9ae34d9e004487b8acc768b943e75d..2ee043da295b03380964a048a363d33ba0e9f3df 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 aadf66c5521b81bd8d6007ff56fd72c0efaad146..490c88a4220ff6729ef03548b2f7eff6a10e3dd7 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 82eec3eecb5c4f19e9da1dc0c9c2d2e2d9a7a39e..e1fa90b6caf9c6383b80735902122175fc103b59 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 ccc021a95756d0907d4f0abea7aba8527fd44763..4573f18614f7f9a3e7df44cf1bf1abf2326ea091 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 b76de536ee7110924bb05b528fbfdfaf234f528e..8c6606cc65636dc4091d73f09115b61bf11b61db 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 807b5f200467b8fe766651769e26fb2dc0398db1..1b7dda307a9f215e4fa3df141de16adc2a6ec9dd 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 0772c5ff6542ef67c230cadbb64afa1aa45e69ba..5af833e7d639ff6e33f47e655963dd07c977a3c4 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 f295b509252320d7bfd2ebd0a0337b848e6bbbfc..a928de1ca420197791fd00b8d5291bdda19377dd 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 e40fb8448adef7a614579bc5a10a9b19c02fb5fa..49c3e5d75baeb439558a1f018c47fc21d59ddc28 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 53b6037e3fe664275d9cae5cf4d9098f5060580f..a1225d2d74ef6c566dbabe4b5667352780e51d44 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 de96c38b1596997999c83be982936497ffc4abcf..c807d796b6ed0c0c4e264790ce9f3e15f18fc90b 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/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 0000000000000000000000000000000000000000..e28e5314faf4041c8ddae896572bc4ac15aaeadd --- /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/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 0000000000000000000000000000000000000000..38909739c998fecd83b97c2da80a4f3157d719c5 --- /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/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 0000000000000000000000000000000000000000..62ed8290380b10265dc88009eabc87cfeeee1a50 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-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 = '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' + +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 0000000000000000000000000000000000000000..3193d2cc9ad9cca352af02aa63bded0cf1d2c3bc --- /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/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 0000000000000000000000000000000000000000..9375fca351ab8e8781441b71242ccd7bdf90d736 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +# 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'] + +# 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/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 6a204cb330d2e870733ddfaca1420e2ee16b8d31..f95dd72e441a13c96968efd4fbbce63e0a327987 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 4c78a146fe847df2693187cb1092e41c7ef25fb3..028fa649be64e3b17d080c5859ea22f71e6d75cd 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 c44ccfe556db5081717276ddbd2b3c0003a683c0..e460a1a60c0c559451d210da7076e0d93c0dc5a2 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 001ee2403f61fcd804fdb3933913630e568640f0..7828e8ee3dfd8f795afce16b6fa0d975595f7bcb 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 6178aa2f65b40ccc344f54fa9a71ae984b5f688f..209842e7274ea8cdc07f7e8cc3e27723ccfa4195 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 99cabee972a90f554bd776a148892b405c045992..c4e43d9fa92acd8307964353eb25ae8670fa84ed 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 c4adbe0ae3d04e6cdf7bcda3cd6a9a379e5aad0d..9b5a71ce36a396a3eb9406c2ae9f3c8ff61e24d5 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 2121a1a6d970db3d7ee1fce8ef5217395e8ee332..36a86386a0c1929d933893f11441021f81eb08d7 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 92c9a61b43d435239cb6842062493ce7d727e4c6..3f28cb9676e068343a58137b9978e91374d97a1b 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 3cd6a1805520e1a3a56ba8d18e4c4b9f5f9d4afa..ee1796488dc2cc27dc7a3947ac9fc26ec98600c2 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 22f06996499109fac8f8d176334110a37ac5f868..97573c0075fae5d46bc83d5b2a4fafb1bad3ab4d 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 922aa7934403f90b408e5e5dc91e7a8ffe870e7b..55248460835190681a3d36a0b6d4f478c1b9a020 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 b7639d24d107fa60b148b16ec7dc3df2d1c2a8e3..53016847355b8ce89c6a378b0b1c22428411735a 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 21ed19633fa70499ca256135c91eb55a05258b72..3eef4c39b603e09534b6391b808f90ca8caf4024 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 da5a2ab9be42e9c5ffb09be5545117290b39fbdc..de266ab029ce987ec62d1ac325bb76e794280939 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 9e61812d8f1b1a77516a1fbccb6a50b3651e1603..81b707143d7bc1d9fa835f690b35b41aadd7297f 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 9a3879ee53e8476716666986083a725186585a87..91e7ec80d3959b8c18528ca4d0cb325ae8e9a47c 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 5e4968df608158a37166339daf1984cbdbc3d6bf..3b51024f129eaa183dbe59c28d20b7325ec83627 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 43cd007ba43bd6bf2411ba2ebcb287cdb0c02fb0..7b345a78e734e6545ee7dbc855c9799c92080d40 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 28ece27457b57d106e842e82d4eec2d87bfa5a23..154d705ccf3a683ba65c3ca2aba457d77123d18a 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 6f2bcda1cb37274a73384bc0acd4bd9231cfeb45..952a3f2313389457475e435f4d2b65c896b9e68e 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 a9d198b99f773ec4b52ff95b7a79b82ff96cef2b..62a9caf2eeb7fe3dfa6b60ea4bdec4447303cdbc 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 25f7950baeafb7667c77626ef2db9e323e0f0902..46722880e780ed3a1416d3c6b5ce15bbed7b538c 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 df72fa53c0c27b8446a3db9f8662a14bc3761102..452ab3ddd5dbaf91c9ecd99e6027b80fe2ca2853 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 4b32c5dbb286f49d4bd015024ddc00aadbef27a2..7de5ce16aa9c9b9bd97c902903a126f435b0a731 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 c247bd8cc678cf1dc8255a6a5a30c563e27c49d6..51baff5e351e103b64f378277c0905bcd335805a 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 362bb90b08c99b2bc0fc95ca8f6ee9c928acffc2..51936e972d63eb0827fc2fb72b37233d4cba4319 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 aafd77aff0845b7ca97f1792a83e640b0b4abec8..8d146fd342b61c67594eb2f3cdcc1d9c1a1a712d 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 9e343efe2eef59f2bed2040ef5b44c3426453923..af79fd719080b8f72851f1957106d9fb0bf57dea 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 da4a9937801dbeff8aa6dfdaa45c8dae4c7a19da..6042d117f676b54742c1a13292535395fff03552 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 57c2903c5774d8af57b1288fe7268e3dc8431e69..37318d67374e58b7d1167f6c6261bb91c96d6980 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 d89452f540baac252349b1ad730f7ddfb561ee64..42ecc0b6a8d611dc69b32ff1ae2010b7a4ce5b71 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 1bdbdfe846f2f8f02f5fd53ed0e65c319d326b54..82213850c001f5126229b7ec2f763722762cf296 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 9d433db3c415c4c7e5f727af2fdb557095055d2d..2cc20c2772e72ddb450da77fcd9e6968de64ed90 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 ab8507944b70dc74fe19bdc576eeda1e49e14b52..a5c22d20a4c968ac60e28b0b65d3710dabe5f8ae 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 f154fb6c65b3e1464e18ec3295021bbba589b200..fc731e26eea8e4dad6554e978ce27948852546de 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 2cb7f99ce4e56b7d0f2ecbbed94ae5c9579c3132..702e767c2348f19602cdeb6459e1779d51d878c0 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 e0b4b71ab1ed505936f260629330b5a33ac57ccd..dcc37ce659b00129b3d5012294796ffa3d37f0b6 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 241463337ade35a799291414d6639fae0179ae29..2f03a7cc46ed2e2d8ca5b359fba60d79a701b82a 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 37f96fa0142f3ec8c62dccdc39faa7e88ad2c41c..7c51ee293844b88cf6c2832931f44ba596f9e0bc 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 41552f25a96abc21a8c1ddb116a54f7dc59303b0..535ba2e73262a2d0a465175f536cbdb388851718 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 4d1e0dddac5b2974f4488b8ced16d846c81657dc..904f548c975578c06f4c15f1c364bc44d6f1c9e6 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 aa6be8f54d47abbed78a8663231c9374fa380a85..c7bc45badd28dbe2bd5451b64d21512231f37532 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 3de185ca6388eb7dc8032ea2e1e6595a7caf6f9f..04c3682224f6a99d602dfd4a9493f9e54b19c62c 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 1de4297cceeadc693a73588b680f4c47234c198f..fd9c783f5306ef689746f2fb1f9d422e6730bfd5 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 c858c20f5337f66f7869cbd5b86943700d454df2..5b6fecfd23a9e3fd22f05dfde7ef8c0671f6ffe3 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 92aacd886cb8392383012810ad3933f00d6f5747..5866da643e89c2151143accc9a6fc8ad75a30e39 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 ad8be63148a87d6eb827c77331cc04190cc877eb..a3c48fa4ca78fbf2040c32b4528f82cd9253ba22 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 9993bc8e4708c7117307c5cb060e8c3d0dd63298..10392160f182fdb57b096d294192cc4624603ddb 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 new file mode 100644 index 0000000000000000000000000000000000000000..e39d8da94800c1e4800175d4f6a070ffea27a5e3 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -0,0 +1,25 @@ +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' diff --git a/easybuild/easyconfigs/i/intel/intel-2017a.eb b/easybuild/easyconfigs/i/intel/intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f1760e4271686e844a1674a057d5c647f1da3319 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017a.eb @@ -0,0 +1,25 @@ +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' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index ac6a734e6e5e2ca6335058c415243be07c7e3f9a..14c19568ad7d886d76e875c9896634cfae96ab99 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'} @@ -16,7 +17,7 @@ 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/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 0acb163cda03df350f6cf8ddf755ede403528e2e..4d7b4439013c54dad2ba93b3b77b361b5cbf076f 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 8fd4cb48f890bfd83f5b2fbede260b484fd10d36..4d3f41da1064b2cd8c7b6aa23b0b819e06de4e6e 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 9d67e520661f177d3acbb9427b4175809ea46dab..74d4ba917ee5272fc847b0299ecec670e4996a9c 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 aa85e82a98aca36f1f88167d7fe6405ec3cc0a68..a9a545eec79795d16c665388a3bb7bdccac242d9 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 544ad6da2e722b185c5f27ff40faa72d0254eac0..e17fa43dd236adb6a24882eea9b9a8fe3f9ab03f 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 f9059cff3e13d56394e026c59bbc90ddc7ee74ae..93dbfc98f8005ff95e6346c0a11cbedf290abf28 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 54ed73649a82ac957b0c23edce844f606f677b99..5d1d7432421c168617528930573158b98e63d561 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 cf9954cf88316acdf02c8c9abff7b7dce5e4958d..ced0e875851c4b9494aae937fcf9cab1d9937264 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 6b0377e8e38cfad4db53a54c3c390e39f4bb08dc..f0219ff350b95edd1a82dc78de498581ae91cdc2 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 6039ebaad32a322be08743588d0db8eaf6b63ddb..9d9e8846e679a92e0a08b02571d0184f990ffc01 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 new file mode 100644 index 0000000000000000000000000000000000000000..4d75373f4f9eb8bf5ad6fc233ff1f49d7c52204d --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -0,0 +1,22 @@ +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' +gccsuff = '-GCC-6.3.0-2.27' + +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-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 3c9854b3e19ce4561dad5987d8fecc449e974c9b..9580ff5296df326b72ed4d0e3bca4e9988aaed23 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 6ab1a7b7d5b8f606aa521a0e2e8f78eb664b81de..db8c7fb2afb5a96e5fa64b157417145656eff4ef 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/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..571b319a14d045c067f510b6ab722fabff93e36b --- /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 Open 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/i/ipp/ipp-2017.1.132.eb b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e78bfb109fc6cffb1224e8983a7b7d644001386 --- /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' 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 1497f12bc7e5fae5159863baf334462c4c48f4ce..af01ee3cccc95db7431f02c8de34d05e7b840113 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 dce7087021f3d539ce584a89d43eae36544d9e69..2df68edb57cafaa49b593180b7cbcfa7a580e117 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 c5381d564c98e407cecf5917c70115623e147920..c7f19f61c1e8aa17c422ffded5fff0cea39ccb66 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/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 0000000000000000000000000000000000000000..ecce4b3046b5665d7eba62277c4f8c6a7a417db9 --- /dev/null +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,112 @@ +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'} + +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 = [ + ('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'], + }), + ('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', + }), +] + +# 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/i/itac/itac-2017.1.024.eb b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4c7fa5a53b3fc4a33c92c03f0fa44fbd18af534 --- /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' 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 b8febc89fcbb34c39370ee157951c8c83ef45177..5e7c707582951724b609426e46821bcd9cfbf4b3 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 67482320a65ab8125afca21a81bdbfed76456163..546ec4036159cb7d901f68e6f6ffb3b0840fa995 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 42551d67c61cbe07655d8e131ffebaf6c7cf032c..89228066326e0157f0e342d8749917206d4dc79a 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' 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 0000000000000000000000000000000000000000..363163f77e61a638ef110ec034a73049de14486d --- /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' 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 0000000000000000000000000000000000000000..43aa70ed7bf1ed00593c7159c1ea567042ef19e8 --- /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' 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 0000000000000000000000000000000000000000..57b073f549f2b24b30c1c608a588b8559de6922a --- /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/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 0000000000000000000000000000000000000000..80e537b9bb171902768836bfe257b24b7188f78d --- /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' 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 0000000000000000000000000000000000000000..23bfbfb00d4a9b8b35f7511bfdc260bce417d6fc --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -0,0 +1,25 @@ +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +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 = { + 'files': ["bin/jasper", "lib64/libjasper.so"], + 'dirs': ["include"], +} + +moduleclass = 'vis' 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 0000000000000000000000000000000000000000..668f15ccada8615bd6b6edc69f4753270231b710 --- /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' 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 0000000000000000000000000000000000000000..f95da7cf07517f914596e667f966140cb08a12ce --- /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' 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 00bc8cb97d9e349ff8551f3b206b12658f6e9ec4..4dba96087d9e1af1bffc9a93ea41ea30a0cf573e 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': ''} @@ -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 $EBROOTJMODELTEST/jModelTest.jar\n" sanity_check_paths = { 'files': ['jModelTest.jar'], diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index 91946b388ee31943ab198bea6c2eb14bad9ec950..37a4b9dd9abf3227d611a7125a108d1b3c96b635 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -9,7 +9,7 @@ name = 'jModelTest' version = '2.1.9r20160115' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -26,7 +26,7 @@ dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" -modloadmsg = """To execute jModelTest run: java -jar \\$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/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 0000000000000000000000000000000000000000..45f685672f8d456f1b93eaa63ddfeaa583a64376 --- /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' 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 0000000000000000000000000000000000000000..7f4e0024004675607f3623d23ad9d76f459c8d2f --- /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 = ['%(name)s-%(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 0000000000000000000000000000000000000000..3ae20a25b6770feeff68c9efa2dbdf0d4a48e0af --- /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 \ 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 4bb09cbfe2ae21d6675f245aff4201cd39948460..02cc25cfecf6e5dfb5ba2753c5712d3fc0f5d903 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, @@ -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 8814a7c92cbef3955d474ebb1098385d6d42aa30..af61c387aa206a5899f41822a1b8deae1e6e484e 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, @@ -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/LIBSVM/LIBSVM-3.22-intel-2016b.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..26b2999f95737276426c4f1e953c54d5528ec60f --- /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' 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 4228c8e8243c4ddc393194e9a4d8788c23a7060a..59f694676c3cdbcd8f8e3f117c758bea44c40ccb 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/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 0000000000000000000000000000000000000000..5fba0f28fc4cb6687f8000afbc67d2a57b44ffea --- /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/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b39dd8a48bbb3e57dd2371c5c9d9842fa628031c --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.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': '2016a' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-%(version)s_fix-Makefiles.patch'] + +dependencies = [ + ('HDF5', '1.8.16'), +] + +files_to_copy = ['bin'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/lsms', 'bin/wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch new file mode 100644 index 0000000000000000000000000000000000000000..191092dc63f7557fbfef36a2741936ad9d3467e4 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -0,0 +1,108 @@ +#change PATH and exports +#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 @@ + 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 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 0000000000000000000000000000000000000000..801057a84fa90dcb07a4f77b08cb1e37c0f00c33 --- /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' 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 0000000000000000000000000000000000000000..dd21d5b9aff93edc1b94497df7b4ffc62a51824b --- /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' diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb index 128c5bbc07bbdc51f814b4bbeea20e5d339881b0..27a91f92c02cab36da3882280f50f41b0feefa2b 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/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb index f3fb0f0115443177d356af4c05f8b351649df7ac..daaaa15ecdd865c3439c52d1b80dabe70ffc5d34 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'} @@ -19,14 +17,14 @@ 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, ] 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/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb index 5b2c252b76084d2497e44c2424b0dbf7498e78bc..36759b619b627fbe18181c72f383bcaa46536fd9 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 d18fddfba62a31d9b7e7d6b3d1c690b17da2c8d2..245af77e27e00223d49c3c29f2b1194d8ee01ba2 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/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 0000000000000000000000000000000000000000..9087c14aa4e6c72a983006293303c5bf4210ead5 --- /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/Libint/Libint-1.1.4-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb index 173c7dbd1eabf1c02320c0a86e2eb4978944a812..534b88561a891b23fd2e0c10bf0c8ed488ef623d 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 ef47d32bbf871beac14ce45ed1a199c5eb653442..deb21649418330185c70ff551cf7c65396455732 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/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb index 56cf148c48df8b112d85d0dbe91aaca049655e72..593afa9ec49bba45c69fd0a1cbf6e989e0710c67 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 new file mode 100644 index 0000000000000000000000000000000000000000..928179dc391f1bf24a32e62e479b861fbe6c70c0 --- /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/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index accf89b9e8944ce9c93960b8f490434c441896db..785074f0f99c1a9d563611713a5c836b2700c108 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/LittleCMS/LittleCMS-2.8-intel-2017a.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..338a40a66dd9b651d25d823d4efb523921281636 --- /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' 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 0000000000000000000000000000000000000000..d56882eb94142ef25d11b6e08d767a2af28c83c5 --- /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" 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 07ee05389366f94e66cbe48f755dae163fcf2587..9297cefc7a0894ced7256e201f00224a4f81c2c3 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 new file mode 100644 index 0000000000000000000000000000000000000000..9301b8c32df3c01e698d525a6284d40d86d80c02 --- /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/Loki/Loki-0.1.7-intel-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb index 353bbfd9402a768028ef1373e2e1cd88827f0cca..fb4f7b4645c762b63b9d5550bd7140ba1902d7f7 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 a25e47aac4fbfaae99f635c077a2c19fb096b4b4..a61396897c4b813fe6df552a0734eab0ac832c0a 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/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 0000000000000000000000000000000000000000..7dff23850730912765846f572d0de20e79b8ed40 --- /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/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 0000000000000000000000000000000000000000..faac09818810829edf3c54f7d93ce2d562c37235 --- /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/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 0000000000000000000000000000000000000000..b66d7bd7680719bda03e9106bfa81ca3ec435ade --- /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/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 8b0e336093596de3b852b87c8fc84d6244ebe118..b4b7228f141c1df4d289e4fc638759310a02ab76 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 0f718686632e59a349ead0592226301dae3d44e0..bc42f6068694b0ff73ca39e596a3738c299101ed 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 68589245d1f3450dd0cbc0777d51fa734e804d1d..0e450049079b91ca334b59a95373ea94eb779b71 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 60cd626d31f6380b26c3d664c8cde29a1c284192..2316d701754fa9d8606d268e9e6cdc816551c96c 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 ea33d4f1808c86ff591f1961ff50843358527358..e34d4affc3c41c7c63815a3d864014d5b9f294c2 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 873ae3da80b4e0b797043e11aeb81eae0251f2ae..1fb8f730cc9731992f1306bd9b8f6c661e6269ba 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/libcerf/libcerf-1.4-foss-2016b.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd70dd103476ab0285e8e305b3778f36ef24fed0 --- /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' 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 0000000000000000000000000000000000000000..6a1a6a3a084ca603b3773c2bd48f4757ec5660ec --- /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' 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 0000000000000000000000000000000000000000..8604d2ba030f2e3ba85db3e3a0ff41445a891ae6 --- /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' 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 dc2d40a9157369e7e89af9ba94b2c3eca9e9aee4..749889979407c157938180c023a01c419dbe739c 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/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 0000000000000000000000000000000000000000..a8a5a109c80fc8a68bafdb9d62dc04c918de3f69 --- /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', '20170314'), +] + +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/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 b12575ef8969916ad060e1a2d24d206771458aba..ce89a700f082150648f2d4a7d5201b93c60517a0 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-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 0000000000000000000000000000000000000000..e069d2a221adf957e40bac08a2fb323da1bf1e42 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-5.4.0-2.26.eb @@ -0,0 +1,19 @@ +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/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 2de9d3663c6cbc00a42adadc0789cb496578f69b..fe73b8ae707818c194af984e5d3a051e37409556 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 3b555aa6f7f7695a711e40ec9bcfb70114de30e0..7f0cee0e30d2b03a84dc2f6ec0d305c8e8d65a39 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'] 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 0000000000000000000000000000000000000000..41eaa5ab15cb752f8591a3df740cc73dee8a2e14 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -0,0 +1,28 @@ +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/%(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"]], + 'dirs': ["lib", "include/event2"] +} + +moduleclass = 'lib' 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 0000000000000000000000000000000000000000..ab5a66564f9b1fc82dd5afbcb5c7eafabb91fa6b --- /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/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 0000000000000000000000000000000000000000..af1365b9128a458641a86990258988438d25b2fa --- /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', '1.6.24'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' 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 0000000000000000000000000000000000000000..2b4825fe33708c4980c4786d0849d6005ca06b86 --- /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' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..c2a203f1b2df7719659490f63eb38a9588d616de --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +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': '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], + 'dirs': ['share'], +} + +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 0000000000000000000000000000000000000000..921c5c073d047ec0ca8694a128914ea60b221ebd --- /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/libmatheval/libmatheval-1.1.11-foss-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb index e1b1e8de360914306a697eadf9804345c047e38e..87e0b674879ea4a8b0243283b9e10a1309538a62 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-foss-2016b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae6c12b340aa7e987152685376a24a1b7b65b58b --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2016b.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': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('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 $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d721e0ee34e02240a530f69135b931c39fbac85 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$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/libmatheval/libmatheval-1.1.11-intel-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb index 61dae0d3d6a1dc4a92617148a4dbc5a5caab654a..d95e44d0d54bdd9fd74d875ff7193a384584d374 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 e8c49e497ec884bcf9dbbe639e39271adb489485..5cd1c4de6656aa4ae909d9d704e4218a6c2347e7 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 1e97665ea81cac89541c4f5daed0fe495d5052b4..f3389388aeabf4104e69ed763ca5dd00621b0fbc 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 5c4d14cc828662b693c8a158021412fd5109c9aa..30524efa1491b250d50d6122722d9e5919b28f05 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 69e1e6bcedf93b9529f1bfcc3226700299c84c18..5b8915269a4064b8867c5701304c354b4794bc8f 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'), ] 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 0000000000000000000000000000000000000000..11ed8ea67dc3bb96c1126c0e20eb3dc201fee1cb --- /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 0000000000000000000000000000000000000000..9124b553abdb16d01be77dfaec2b668ae0bad414 --- /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' 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 0000000000000000000000000000000000000000..2a604f301f0ad1dd8ac42c3dde33b6ae1f63e604 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +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" + +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/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 0000000000000000000000000000000000000000..15f766ff31e86124c1374441d486ae4e70a884be --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +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" + +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/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb index b76c98f402c7edf7b69faf1a9aa3066c2151dfba..7caa32f2db988b7f283cb1daecf38c4787db4efb 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/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 0000000000000000000000000000000000000000..e0204f68810887c2cfe834b1d144f2153a2ca2a0 --- /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/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 0000000000000000000000000000000000000000..3d37620c501bbe2906c589e8ec72d6a77856312d --- /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/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 0000000000000000000000000000000000000000..7aca3fe451a83b547862075ca4d9a2db4b65ec1d --- /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/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 0000000000000000000000000000000000000000..85ea50b7107bd60abd739c14736635bae3e72d52 --- /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/l/libpsortb/libpsortb-1.0-foss-2016a.eb b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb index 41eb85171a98b7488d3da4b5a1ef4cb59bd0270e..49ee1596052a02b60f7092d553d1b55036c77345 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/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 0000000000000000000000000000000000000000..3f5229b1357f699788f39dc7e69a6ca13e9d59c4 --- /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' 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 0000000000000000000000000000000000000000..132a89cd1e7c412313846bb175478a59abc813fc --- /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' 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 be707f2f9def765fb3b3eaa50dadf0498be34a17..6d2b145e5dfb59153307a21b9ea95e1639402280 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 12e011a8ed784f28fc302e0897afc9a56185dde2..ade9c01fee632061b1cc3b348ae775b1ab63df0c 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 1710b5c8bc4dce739def12e8db8ced5fa616e208..870840254167524df553e4b9f5e7b580e26173ab 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 a4fb8619cbc8911dff1da7a7048eedddd9ab2804..7bfc1d634ca48abbe319727567189db932dfd652 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 c434630db4d4707fa07e9a6982c63946512afdff..33e6e24615e05cf04932243cfd5ea48b9866c9cc 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/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 0000000000000000000000000000000000000000..f4f4e99acdf056bc62fa6c69b33b73a1f3bc0ec6 --- /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/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 0000000000000000000000000000000000000000..66d703c9871b4f028c188007f742502ad15f6534 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -0,0 +1,31 @@ +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'] + +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/l/libsmm/libsmm-20111205-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb index d7907d8655496fbbb0ae929c29e25f8d06ff419e..ca93b0d47a91997e7a0a4e362cacdae1725eecc6 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/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 0000000000000000000000000000000000000000..faf9cf93a161b8734f13dc840a05cb6002d4cdc1 --- /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/l/libsodium/libsodium-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb index 7c1505061ba59e50f8594777d3f8eb116a90b715..ad64b7cf37645ef8367207cab81b3554fc2c0d9e 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 = { 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 0000000000000000000000000000000000000000..5ff79fa5a749aa6278083c0bf656bc723d4f38f2 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-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': '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' 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 0000000000000000000000000000000000000000..04f41e27d349f9ab8e3ec4f70e29498f2fa53923 --- /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' 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 0000000000000000000000000000000000000000..c87d185cc10c0f8e6ea7870d0424b5484c072f27 --- /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' 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 0000000000000000000000000000000000000000..69d644216e5ad9e93572368002305492eda6033c --- /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/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 0000000000000000000000000000000000000000..677b1630917974c76970485eeb253d92f582a714 --- /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' 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 0000000000000000000000000000000000000000..9e72961b6bdb311e7cf06adfb7ecc3c04c76a567 --- /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/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 0000000000000000000000000000000000000000..83d12ef5f80dbf5498a84a4bc725d655b9d2417b --- /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' 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 6d7bea7d3d375e9962e77f668d4a3ac104470d8d..5c7a628aafb6365ac4d75dd15f48fce9d65ed344 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 3c6b226b5a25dfe259d993ddd2466818722152db..57b9a33b63a402154dc546053bc5a5415537e147 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 052063704a27337eaa7379021de783dd94b3eb79..25d25c5148ecf208e1f5296cdfcc110dd917761d 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 19e0b26c921b9ac7415367241745a8fb07588350..bf35428b39933125bfcc0bf54252b3517b49cb02 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' 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 0000000000000000000000000000000000000000..9d6b0fbbc4eea3324b1ced5c3c4a96a59916d3fb --- /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/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 0000000000000000000000000000000000000000..fdee6f57685e08847ab6fca847beea7066d01d3a --- /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/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 6bc89f03e758c89c71eb1d8fd7b6cd8ae5096000..396cb5364febc942373f0b5630299f55a4c291ab 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 +15,14 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] + +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 15053fb3db8820e958deb64c2aef7d2458505c06..19a10c83627a3199b4d66955dda4d71bb3a668ab 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'), @@ -26,7 +24,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index ac65492ae4f28425f21352e8c628fb01b109200c..9cbc7f2bbf4a4d98322e7780db540c71c14b6198 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), @@ -27,6 +25,7 @@ preconfigopts = 'export LIBS="$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 6d87f1040086312119a937e3edad8d178b8775d0..97bdf4390624b05886ea78a5ad94595ef2b14176 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'), @@ -27,6 +25,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 6e07f1886553648b16d9cb5f92405a5892ee4b57..5b2faed5579d8dfda3ed10078d72c995e7aff0d7 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), @@ -27,6 +25,7 @@ preconfigopts = 'export LIBS="$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 aea3c64e514e8e1c8a0f6ea4a2e611552eca3b4c..ba5d70976962affc27138d258b9b893fd9d1c102 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'), @@ -27,6 +25,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb index bd766f2e399ee2fca5e28f2541af11ceb41c9fb9..547b2c04e038abffddb30716bbf4779ed40fee95 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' patches = ['libxc-%(version)s-fix-initialization.patch'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb index f86e8ff9fbd84150b41751dc0988368e93f6fe99..ba87bd535c26ae057acb1df7e503a81b0dd0d1a2 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' patches = ['libxc-%(version)s-fix-initialization.patch'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 4c45b545b5f57f417c6b322c76e45f7c4611a2ac..e944b72c188ef4b9bee8fb8bd041eb8fe27e427c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$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 8276d5a07e336ce48c6f5d25267a921f68590f05..b9e898267154094a54feb8d0398b5127e3d7720d 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/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb index 0bf711caf0e7a9f6e2038fa8e5e6c7b3a54a71e4..8bd05d53ad1c1417f8938e0feb7ca34857fb1a09 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared' @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index e6561d3ed6247b822c632cf1a9f3be9359fdfd6f..22e411e0a370055cf8e55bc3553e8ff2e031b217 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb index c631b87e66aa68755afaed3cb36cfd0eeb8d8978..51c0a0a535ac7a08bfe2322ba262baee5ce39724 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared' @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 3bee3b3d9c155e4a66d230644eae39462c14e7bc..45bb52f70b4d9de891e8485f5581e985662cd3ad 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb index d9d2ff8c6b3e99c6d19cdb9a8fb77093735737b4..39dc38965a8ab191c40987ad6b05329aeb2b7a8f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb index 254367cee7edc335d841ccf23272bf1a76b38851..3ce46b560945c86571f029a8ab3af995dbb74715 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 13f7f941b6fa261a0cece0a4a40cf8c8b2596562..3958efb9f5374c06de258c9ba34d1be79a801c34 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb index ae74d150b04e7c568340754278cadc07372aee73..3d0a5a1ed8ef5afd28970bbe6684162a95d1dd97 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -9,7 +9,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -21,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.so'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb index b029d7950cf262fbb5e236df5401c2f70accc737..5df850f9998ce55be61aa6a2595ba012c12aac66 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index 7590c8664b53f7a73aa9b9a100db3725781a4b88..a3e00b811aa5a8fcd0886350d9dac4c5d1cb3dc7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 96aab1d17858a1c410627bb2d3749ceb7e9dbb8f..3dc273ca2e74d3afd5e63be75b8e42ba357f70b1 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -20,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..37456a8225492750d76dde22ec13f4b361e6a03a --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +# runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 4f8d72a6348448066ad51e5093f386222e0a0904..56fa742d7d8237424d5fea978c3b7b2b16944d72 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -19,10 +21,10 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index a8378f30876e07fe358031c9e97886218e07434e..0fb5faa09c35644b4bf2d7fa354dd8b06e1d16a1 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -19,10 +21,10 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index fd83352b3068984fde6c1590772f4d38bec2a18c..e96102336e491e79b227b334eee626352977d497 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -19,10 +21,10 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 951b7f060524ccb3711edb6bd9b6bf5ae92a9d79..df3c9b9484ef7ed4f4bab60fe809069429c66a28 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] @@ -19,10 +21,10 @@ configopts = 'FC="$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]], + '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/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 6921c06b50d83ae461afdd3b26371472e504b9f6..58524fdeb0ade00d51e06dbb8560a643f94d4841 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/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 0000000000000000000000000000000000000000..b71554c4dfa26cffc41523ca8e3a7fa237391375 --- /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/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 0000000000000000000000000000000000000000..8eeb4025478e62f7451a32e463cd749cfb1093c6 --- /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/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 0000000000000000000000000000000000000000..42e7a06480288d8b26d5743a21e9d9833778d007 --- /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' 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 0000000000000000000000000000000000000000..f4d92dd6cb4d91285e52906d371d87d61c202b67 --- /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/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 0000000000000000000000000000000000000000..5436a17dc9b6ff009c9939fe9946bb1ca5768055 --- /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/l/libxsmm/libxsmm-1.6.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..84183281804601601f44601f2b88fcc949c6b06b --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.6.4-intel-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': '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' 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 0000000000000000000000000000000000000000..44f94ecc3d0fc918b616ca112d57532b4103296d --- /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/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 0000000000000000000000000000000000000000..a5b92f3bfe6430a2603ff1f955140780b3a077e1 --- /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' 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 0000000000000000000000000000000000000000..735ec88bea55b87984a87c828da367ab76308592 --- /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 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 e70401308cb1aff385749a3bd0146c7d75ca786b..6d16b1a8fec42e3e459ea20fe8fd29afd566a1e7 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 +8,10 @@ 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'] + +checksums = ['cb936aef812e4e463ab86cbbe14d4db9'] 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 2b02e64ab0cd4d1759c1e72c88d48a85f8f57504..00b6eda6687241e7f54318a681d4dabdc5b6d5ab 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 +8,10 @@ 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'] + +checksums = ['cb936aef812e4e463ab86cbbe14d4db9'] sanity_check_paths = { 'files': ['bin/lynx'], 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 0000000000000000000000000000000000000000..c1c1439bf3cf0cf7590093428dc22da70b45314e --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.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': '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" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 0000000000000000000000000000000000000000..ffbaa7a77a230679ef26403bdb6a9ae57d94633b --- /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/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 0000000000000000000000000000000000000000..18394615f92cd33ca3aae0475956c409fde5a6ec --- /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/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..f186b0ad857e83e1c7cc8157e211c6102c4ffebd --- /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/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 35b0a5d11b4ae3da09ef4b5a688b5966e77871f3..f41f912592a8f15dbc7de811e86b81f4bdd8007e 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 @@ -24,8 +24,9 @@ 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""" +You might have to adjust the requested memory +""" moduleclass = 'cae' 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 0000000000000000000000000000000000000000..7cdcdee529e40b50b590e420d93502bd9b94aacb --- /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/m/MCL/MCL-14.137-intel-2016b.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..11b922bce75c2f0235e7563e8ed5fb360e7e3600 --- /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/m/MCR/MCR-R2013b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d025dab9a490095a9d641e4d498cf30a0256cad --- /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/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-R2014b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1aaf91935081dc3cda21e8ef00d326c428d0b996 --- /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 0000000000000000000000000000000000000000..02cf05532e7c46ab53e8231dac822de64956f9b5 --- /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 0000000000000000000000000000000000000000..78ab492fb846663282f0d84734e79cd778557ac3 --- /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' 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 111f00bfda2bb536a7698d334934f1139f0e62a1..9b8ad14bb5f485d88cb5a98438f9508582185776 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 @@ -11,13 +11,13 @@ 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), ('Python', '2.7.11'), ('HDF5', '1.8.16'), - ('libxml2', '2.9.3', '-Python-%(pyver)s'), + ('libxml2', '2.9.3'), ('zlib', '1.2.8') ] 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 25d836f8e532a1dac488f9d0b177f214576e948d..9296449814051e3a817fe541b14731451f18aee6 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/MEGA/MEGA-7.0.20-1.eb b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb new file mode 100644 index 0000000000000000000000000000000000000000..4513c7f7b64220318e8099468891e042be55a404 --- /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' 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 c2f466b38e92909895e96027208eaa2c110634ca..2b1ca4f4f3f20c78e3264ebb11f3d97949008b5b 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 +24,11 @@ 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/'] + +checksums = ['e1747a8a47a61d97256884c676b46c09'] 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 e039fb1fe516fd586d281d2316216dcb0930c07e..8c5d271d61589250e8f5defa196bdb4c4139cef7 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 +25,11 @@ 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/'] + +checksums = ['e1747a8a47a61d97256884c676b46c09'] dependencies = [ ('libxml2', '2.9.1'), 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 151037570692b2db27fcad2f653c4f3fe57db5a9..56000b7259ee6fe5f91c966c519bfa8e1458387e 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'] 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 0000000000000000000000000000000000000000..91d00f113991a6be444926d13e7c5f8a4c6bca9f --- /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/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 b6f05aeb5d714d8b9f28bd3bff2a2a08590704c8..25e6d72da50233130d8420092c20d6fafdd14873 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/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 5b23296323609c153956821f81aff57083cd5946..a98288f90013bd344111c317b0c8974b16f95acd 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 @@ -1,17 +1,17 @@ # 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' 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/' -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 77047640bff14a422b775c5a282966e3c32103a4..3ce4130b75b0fa6d923dc005eec0ad830f2e63a2 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 @@ -1,17 +1,17 @@ # 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' 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/' -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/m/MPFR/MPFR-3.1.5-20161219.patch b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch new file mode 100644 index 0000000000000000000000000000000000000000..6b2d11466e9ad99768daeae89333fc6cb458ec76 --- /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 0000000000000000000000000000000000000000..94a62620158f9af5fe2c6b4d331ba05f2b1a227e --- /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' 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 c8deee658d0e7a205e20769344c3c5ed5b670328..6e3b23ba3c47db9b4891bd9f72db96fd6e20ae61 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')] @@ -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 273c10ebdec0227e91ee0d895ea0bcd1fdb283da..8577e3deb428d40a86db39a25f20d82dcdd81150 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' @@ -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/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 0000000000000000000000000000000000000000..bfa4a70408f6ee9cfafa024b667548bf29523cac --- /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' 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 0d8dbcbf471d1aca8176c9ccecd6b8a4e5df78e0..6706bb83e584c61ec4b1da0cf43d6ee71e78377b 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/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 f289c8d654349e1e7fdd48677db0f167bbf830e8..c29dfc7a1a67fe323c61821ed3141972a4e92afe 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 372dd0b722aa1dbf4ec79704e427a2c66063badf..777e5a69e1a00b24ff754356d350c85bd3c1eecf 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/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 44efa704efcce91063ab660dac48bb3382122748..973e13d8940994f53ac7b92dbbf57e276e44570f 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/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 3c30407be29086f304558d46d8556dfac05117cd..b454981b04a8be4d951d995531c838c7ce8269cb 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 250398115a397892ee509d20cf3cc8ba1b216c5d..e008b133f568b552edac02549da207fff20c417a 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/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 0000000000000000000000000000000000000000..9bae4651685e3bbed94f1243a99711afb98aef7c --- /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/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index b78da99d835e73dde489c08ffbf4aeefd4667406..8357cd6199b33d861ee0004c64c81076052967b7 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/Maven/Maven-3.2.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb index ae08a0b45482a84d817e7b7ce2795308403dbba0..8f18c08a6eb95dc28ed8b0bd7feea09542d027e6 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 642c9d91d211007345da3048fc8b7e2e02a5acde..e4b7cb5e43860695c015c4405ae4ba4025b03f96 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"], 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 7235621e5d7eb453c71274e12836afafb1516761..5b5a91c678c8f939cb6df7bb32ed96574936e4c1 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/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 8175c4c179e4bce572a7a83b1ba9451d87ff17b9..e59823b508b2110d56e46544159bf18244cebcdb 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 f2baa1d123df9bd6bd71250e39c6f388cfab5ce4..c992ae6699608363e20ce2bf5c4082d49d0911f5 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 43c0bceadfbd190b60229d1fcd24865deb02c953..4021c0012d169dbf655da2ade26badc483350c4a 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 47ecebdf53a7b86480626dfcbeec16f8763c4b7b..1db1af42c1115898ba2e2b038fc621b90af48d21 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 047324c714fcb36e29f45227996538a1cb86b930..af89a7e145cbae792f046abd8bde5e8a01fbb188 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/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 3f895315b2a88fb07285216cfc4979edf11aaa85..8757076334d9d8cafa01a29e946621ce20d26fd5 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 @@ -50,23 +50,22 @@ 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""" +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" ' 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 592c4a11827077d61adfee3d0b2ae8fdf0f620a6..ffc67154d80a9c8256e9bb316fbee0f7ac9e31dd 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 +47,15 @@ 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 " +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="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' @@ -63,9 +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 2bd0ff0f9444e69a6acf07212d15fb9a40617a3a..7d75f18d6fea315d0f9f9304a536b97f3c69c106 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 +46,15 @@ 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 " +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="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' @@ -63,10 +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 a22cf02d6911f031fba5d7d5d99dcc53218a1e80..346166fe00558d10c8b59aa935331d49f966e3eb 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 +46,15 @@ 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 " +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="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' @@ -63,10 +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 fb2151e5df58ccd777a59541bd14c797a8e0bd5c..9b02d2b02bcee54b8be825d5e4e5333322ebeac6 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'), @@ -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" @@ -50,16 +50,19 @@ 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" ' 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 171b47710c44b8eba7ffb842cca90768e1bec3c0..45545e7c8397bda5d3e81c1c25d226f09a036d0e 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'), @@ -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" @@ -50,16 +50,19 @@ 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" ' 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 3282ad740cd589c6b1feb1b46744ed578dbe56d2..92703769fdd033be57aca55c162edcac75cecc62 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'), @@ -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" @@ -50,16 +50,19 @@ 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" ' 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 a919f2eab90d692a26d0f04b685cc4f82f00023d..61b180d1ef09464c5d5be37b4e4a2854cc3f36da 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'), @@ -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" @@ -50,16 +50,19 @@ 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" ' 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 54f7d8a513756cbadecfddd761e65a42b6e6d434..6660454e4c75b3a9f642bde01010636d5e48b8dd 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'), @@ -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" @@ -50,16 +50,19 @@ 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" ' 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 8152b5bb382a5de704b62c2e15c600cecff34429..8376070490c5350df441ae68714b3c6360fa8919 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 90fd4b08106c27fa8e78f82acaf70efea622644f..2ac60cb5d00a30429cb64071b60be3f2a5f005c9 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-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8bb12d31a371e4738c7116a49927e02c5a883e5e --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -0,0 +1,66 @@ +# 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', +] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] + +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', '20170314'), +] + +# 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 " + +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, + '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/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 0000000000000000000000000000000000000000..d0aae3dd9cd89ede53f473f8e8496afb587e2317 --- /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/^ //' 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 57483e1d4fbf16f7f69e9d3dbf4b127664286558..a2555dbfc0f62b42927d4878c36aba263b865bc5 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="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' @@ -46,10 +47,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$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 ac83c1243a04119a7aa1fcd817230ae911fb79b1..1ef5829725cf7b06a1acbecef69fcf1b5630cedb 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="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' @@ -48,10 +48,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$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 810e10d3bb903027c51806b7843dd986335a4412..6f68f37b53aaa2caa9295f54c85b7476b82af0d5 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="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' @@ -48,10 +48,12 @@ preconfigopts = ' PKG_CONFIG_PATH="$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': [] } 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 6f7d234353db884cacfa4c3086a177c88957bb4d..8c234a753f427ebe52b2323ec53e7b75c135af30 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/'] @@ -16,11 +13,11 @@ 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'] +skipsteps = ['configure'] -buildopts='all' +buildopts = 'all' installopts = 'INSTALLDIR=%(installdir)s/bin' 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 0000000000000000000000000000000000000000..947de950b4e41c6bd143eda0ec8434055715624d --- /dev/null +++ b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-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 = "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' 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 79a432c81fddef6feecdd91f8e3baaf12adc21a9..c6a015a815e6889b96b54bfc28079307e21cde41 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' @@ -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/Molden/Molden-5.7-intel-2016b.eb b/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe23519684c9848ca5d2b9343ad5a63d050a89fc --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-5.7-intel-2016b.eb @@ -0,0 +1,27 @@ +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'] + +dependencies = [('X11', '20160819')] + +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' 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 c80d4d1ee107df67c5dd30b1362f790aa0531355..51f747c203eb7d8bbf3bdccff1f79ab1e15e4c36 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 251958da52a5a8a82c26fc0480764e38117a9e01..678309eb8a141945d01d309631c27badba8859ad 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 22912ecf4ac22e7ef4cd50e038e766db8c832752..b2738fff57780ee250a46d2bbc02f5ffd81fd8af 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 47852f7b9afccf29b6606fd517d2c722c117b81f..3639fc72f42ab7401f7b2d3278fcae11b240706e 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/m/Mono/Mono-2.10.6-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb index 365455df1b7dbd604bfab36be9df48af0c6a1562..e8b59e149403c60fd8a30b07ee09c26b0ef28f0d 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 4b58a5cd7107097e5a08ff4a5a29a97e8a66acde..11e5afa9eedc45c5ae1279bc26d1321414ec699e 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 ea1fdc28134c61ebb33ae50a7e1e6d66b9737d91..5d4a7d1a7d7288708522d18e12b4bc25a3c41c93 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/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 0000000000000000000000000000000000000000..7b8956bcd6df6a2b9cca3d4ef6a44bfc44e66dac --- /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/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 afe163b841159ca2b65c40ae7fabd895702189dc..aa90066de817aa04da5119d3c76921ac87473002 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 $EBROOTMUTECT/muTect-%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 0d2d28d47b19172b742da3751e61ad7f9a8286bd..4774c63625a8e0ddc85e8f72f494a219f84c4d4f 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -30,8 +30,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb index 86bd5019e265e5e39ae9249c4da81c771897d211..c8d608145e1fdea1c64373852fc5a8b2ccb9b41f 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -31,8 +31,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/%(namelower)s-%(version)s.jar -""" +modloadmsg = "to execute: java -jar $EBROOTMUTECT/muTect-%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/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 new file mode 100644 index 0000000000000000000000000000000000000000..52da5ecd72393035adf38d0c0a0207d509928f00 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,76 @@ +# 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' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info/' +description = """Aggregate results from bioinformatics analyses across many samples into a single report""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s'), + # numpy dependency provided by python module +] + +# this is a bundle of Python packages +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_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'] +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..4ca3af6861f5a9ab27bf6a901c4ce9f1de3dc098 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,78 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +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'} + +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'] +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..63966d2c9caa30c19042dd6f7c44b65e215f5c00 --- /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' 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 fdd34a04e13eb6ae2d398cbc50d03b66b93e63d8..4c07b642931d93554601582309d0acc34925b5ce 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} @@ -15,13 +15,13 @@ 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'] 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/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 0000000000000000000000000000000000000000..dd39e28312d774a1c3d913488de13229fd954a42 --- /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' 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 0000000000000000000000000000000000000000..b7d5d70c2df098396b6e2f986799e17f407c4bce --- /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/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 0000000000000000000000000000000000000000..94bb8895230d2b7aa51aa5207f1b46f84d37c855 --- /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' 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 0000000000000000000000000000000000000000..697a58300bda610407d47b466196de63f47ef07c --- /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', '2.6.2'), + ('libpng', '1.6.21'), +] + +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/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 0000000000000000000000000000000000000000..83276fb208b6386d871b21dcdf2823182eea32e4 --- /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/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 0000000000000000000000000000000000000000..fd17adf8c22ab3f4d9f149c1ef3a3fb6b1dc545e --- /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' 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 0000000000000000000000000000000000000000..2f829b07670ebbc72e6efc5e3e179ebf1db6c066 --- /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' 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 0000000000000000000000000000000000000000..def79919ce9feb80eec1fb61146f3eade7b81a38 --- /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' 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 0000000000000000000000000000000000000000..e00702b768c7f3c36a818269f8d46c17308c5845 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,43 @@ +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'), +] + +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/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d549f797705efa8102fa3c095e0d707ed3f93f1 --- /dev/null +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -0,0 +1,30 @@ +## +# 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 = 'BinariesTarball' + +name = 'meRanTK' +version = '1.1.1b' + +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/%(version)s/'] +sources = ['meRanTK-%(version)s.zip'] + +sanity_check_paths = { + 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], + 'dirs': [], +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..cda151feb8818df8e7eb321af7c27fd930171c84 --- /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', '7.1.0', 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' 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 0000000000000000000000000000000000000000..83e5129dff8c4aa5d396a90d33866bb2c2f04c8f --- /dev/null +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -0,0 +1,35 @@ +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" + +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'), + ('ViennaRNA', '2.2.3'), + ('randfold', '2.0.1'), # also provides SQUID +] + +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 && " + +# 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/mapper.pl', 'bin/miRDeep2.pl'], + 'dirs': [], +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..b281fdb6096e4d4a169de39625119e6c1759bc18 --- /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/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 0000000000000000000000000000000000000000..4226d4a6e1ed847bdd66d34c4de5c371f0872e4c --- /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/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 08d2e9759c741018ac7b69eaa73f97653668c0dd..73545656c957c2e83398864e6d2bd019aa285433 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 221229e3a6a8853c0f178c7f7101816768b1c35a..763ccba836aeaa0bce23a335378d4fc130d61e54 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 5d19338ab330d70960ae54b3f6d6f8abb6792cf9..dab01e8798dd19c7fc97ca5077c8169fbd3f9dbb 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 b6703cee3099afdb0d973de768d2723f09f54be8..4aa55f0033f444727017341aa06c5ee370d9457e 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 ee1c58975014abc6ebbd9e9f28c37e376d909503..eb46a80abede11ecd68d85758e01b11f804761fd 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 1673c64e606c81e97a672d02dc07d0fe0d5b604e..62f71cc876a9669d2279ad02cde4dfeb229700f8 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 new file mode 100644 index 0000000000000000000000000000000000000000..1b74bd9124fb534e9fef0e8b271fd26dbffbd1f1 --- /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/m/motif/motif-2.3.5-foss-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb index 3a9a7c7e64cf16fdee51014d6584821f3d548fd9..91ed1606138665c3d7a31c557841abdf2181e160 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 2b7c9b71bd4f3547314375c81cadca7581eb8a6a..fb05915a84a1056efd91dac6050d85c59d75185b 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 086efed6cd9cd8a0485a31db3a0ca34cbbc8b035..1bc0838af6595163735fac36af26ce2cc63b7c10 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 7da0c48dde771f7d63121a9f6ff7b082a5c3737f..e58c648eee9413bef89eeea7c932fe09debee4ed 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 fda1eaa51f751f599eda43a41d7bbb3280411913..933177a5af396aeae81594db1e3aeaccbad1eb5b 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"], 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 0000000000000000000000000000000000000000..2145d8a94c973215ee02f99c81ec221f7df49d85 --- /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' 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 0000000000000000000000000000000000000000..a4d8935beb619f3ef473c28b08bb083670a1204f --- /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/n/NEURON/NEURON-7.4-intel-2016b.eb b/easybuild/easyconfigs/n/NEURON/NEURON-7.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a3e0085b0bd51bbf63644d2e21cbe6e612144df --- /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' 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 a33090c4b67324c26833505642c18ada54798863..81fb2b9ec4b594fec467ca86d0659e30cbfdc429 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 c9ebfcb9f58fe9030b5f0b13de1eec6148e39a7b..4df5eead7f0616a06f4b785b0ada09638517ca1b 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/3.3.4.5', EXTERNAL_MODULE), ] sanity_check_paths = { 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 0000000000000000000000000000000000000000..8d0219a74222f31726c436e657caff230159888b --- /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/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 0000000000000000000000000000000000000000..abf5bbc2772c00c35a6dc60e2e40149569f355da --- /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' 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 0000000000000000000000000000000000000000..607bdc3f75d4f4d91ad2401938511210a6c1a754 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -0,0 +1,28 @@ +# 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] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' 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 0000000000000000000000000000000000000000..27d258eaeeac824332e30f1cfc02cf37d77e6f3c --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb @@ -0,0 +1,36 @@ +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 + 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='] +sources = ['Nwchem-%%(version)s-src.%s.tar.bz2' % verdate] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +dependencies = [('Python', '2.7.12')] + +# 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' 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 0000000000000000000000000000000000000000..5d07c595e701e03960b84f7031269aede27e66f6 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch @@ -0,0 +1,82 @@ +# 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 +@@ -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 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 0000000000000000000000000000000000000000..f11db814aaac94c4463c2973069e2a96c4ec4bd9 --- /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 = ['%(namelower)s-%(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 --help'] + +moduleclass = 'tools' 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 0000000000000000000000000000000000000000..5bfe59a4db65df2756dfe08d6e14c02fbce25f90 --- /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' 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 0000000000000000000000000000000000000000..097f0bd4af5dc2259b39fa8af7a25379686cfdf9 --- /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/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 0000000000000000000000000000000000000000..6b10da13e5645a91d7c29d6a2d1f597ce3fd3901 --- /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/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 0000000000000000000000000000000000000000..959f14667bbd3718aa321c3838f6ff77581c688e --- /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' 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 87478cf832f5e9c7202aa7f0c6116d5b29d03995..8696b556c229184d8427d12286a9db7c512a15aa 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-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 0000000000000000000000000000000000000000..fa3d6fe9634d0823d529deebe76c2a4e8a0261a3 --- /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-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 6aa937d650d348e77a1b382adc58ef1ef7169b1b..55b91cb8336572cbc35579284b2756cf6efcd20d 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 36ab674b3d8c718341c6804c8d47c20cf51727e0..d130575666ee6daaaa1fb5e8c85d28bcf9162f4d 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 0000000000000000000000000000000000000000..2e44c10cb4552522f6aacb6e0a7580ac84ea62f6 --- /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 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 a0f0b6f197829d460796378a2bf93d05029bdcf3..878ccb62ccb955dee2d8dcc8bd53569b0eb382b1 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 fc24bdb27fe483c90e503dc2ca37235de0afdce5..72e540c932364a29fb0b47e736128f101e7d1942 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 49f253f65d210c826640d7360697328b523e6b0d..f945f15bca15772360eaa03561ebd020a392d9ba 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 262ebc70b918d1801205fae5d973ed950294ed97..b162d589ebba495dcac28750fa978beada90adc2 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/n/netCDF/netCDF-4.3.2-intel-2015b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb index 52365b33f33f80050b4cca69eb83e0417b5a2ce6..126cbec2e82b5412d0f36d79cc832107711c7d6b 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/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 0000000000000000000000000000000000000000..24dee36e77ecf07947d2dbeb85b5788c9f41002b --- /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' 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 0000000000000000000000000000000000000000..d30a65ec63abb93c464a9d47e0f0d45dbeda525a --- /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' 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 0000000000000000000000000000000000000000..d8f9e8fc31fb3db53de9250813872e9da1ccb5f0 --- /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' 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 0000000000000000000000000000000000000000..00b1f1504409954edc4f32b05c8d15db4dc5045e --- /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' 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 8dde76eb25208e4ddf70044f8be0369432cd193a..afc809e5852f7c3082cafbec9cd1a6af4509070f 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 488dd6f650b21339163af62a2077156c783b98b8..162c58702cbe761e0292787554412c2f677737b9 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/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 0000000000000000000000000000000000000000..b02123940f061d84564b708d692152c8b0ac5bb5 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -0,0 +1,27 @@ +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'] + +# Python is required (only) as build dependency +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' 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 7d6ccf39997b1ba13d214fccdd4942677d5ea625..01a8bfdf0f6e36c6f6da1e05e3b3db1cd8a53b5b 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 new file mode 100644 index 0000000000000000000000000000000000000000..7fe4d082b36cc43781d352ac5e2b0f9392fbbcba --- /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/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 0000000000000000000000000000000000000000..c6e873dfe1ed49562599519d0eaa0ad56eb15d55 --- /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/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 0000000000000000000000000000000000000000..dc868ad142034fd0e67acb160890c9ede7221134 --- /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' 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 0000000000000000000000000000000000000000..1cddd58e1d1f5b7962b72ed6bd2273f94426b523 --- /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/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 0000000000000000000000000000000000000000..a4c16330cb19c2e89ebbc28ee431391ea866b476 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,21 @@ +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] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' 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 0000000000000000000000000000000000000000..3d09924f96668c7593a0519223e4abfc6f8fbca2 --- /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 0000000000000000000000000000000000000000..b83a080a7d84774606716e19c6f0d1092a5f5fbf --- /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/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 b0f7a1aaf19bb612f53ab0ae7bc42ca7d01f12b6..4cb15251581df066a30db88f28f44852eac07e65 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 d30d6266abf160541580bec17d22186c5b551d58..82a7c41aa7ebb2d5d91e3e3a996f4c3575bb4e89 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), @@ -27,8 +25,8 @@ 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/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 0000000000000000000000000000000000000000..ddc58b8eb3f87de66ed06046f33804487c2f8b68 --- /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': ['ClassComparison', 'ClassDiscovery', 'oompaBase', 'oompaData', 'Polychrome', 'PreProcess', 'TailRank'], +} + +moduleclass = 'lib' 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 a85c46d3f0216ba78937ad53ab1f3eb6f18c6a54..95182fb7f6379513d01047ce27a8f21a41960217 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 685a061dbd6de1e7b6ebe9e22bb72a1cb3e80cdb..a2fb635e4806277e4c5e34fab461bda37b35b080 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 7d277554957a31f99daa6cbfd699ee87b539abd7..9cd49048acd68432145e3212ea03efac504249ec 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 6a633a98ef1f743e289bf3572aa59fd65462b974..82c2d0b54b39d59ab5c9715a5d6518b6a8bec4e3 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/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 0000000000000000000000000000000000000000..c9312c40449cd838916b3f4cd03194e8d1578bb5 --- /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' 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 0000000000000000000000000000000000000000..534dc92f9916ca60d08f2ee97655d116fcd1a553 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -0,0 +1,65 @@ +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', '2.6.2'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20160819'), + ('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', '2.6.5'), + ('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 ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +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 0000000000000000000000000000000000000000..872aa06961dcee9d78a38019323048a60c83ff0a --- /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 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 e3cd54d745a3b1dc887cca1a45e4e546b193e058..26fbd9394a27708cd241ac3e6559497dcc93739c 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/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 3a54e8b3b2337f18c41d89a43c114b84cb34b61e..8e7a8e3488a8decfbaff60962e035acff4870b1c 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 870b4ca0ecff56fcc0980892294d42c666c30a98..1aae2d7107fb3ce108e57e1bc0bff8bf632347d8 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 1291a991d11261a1ef9ad8955479d370c6dea2c0..1474c30ba6c2fc80b9357f3ff28a77c58d62cdae 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 fe4211f53cee07ecb3e5b9109d38fb5b9c405c4e..e83941b54cde92d11e8fbf16b0d158c5388ceb92 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 23704a985eddb9b5275e0d10adf6b98ef2576c43..9be631f2d33566c889bd9babf01105e468c77cf0 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 b11768a1504a439bf31ff0bcec0e0e824335e602..d1b44dfae9020caa60ad8dcc5985ab703258cd28 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 32dd146e23ce19679a6291af717916733094b43f..1c0d99523c731f92a33c9d8fe5a38a9aca4915b5 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 abbe566e013bd20e4cd08f884d58b34f9fd4e360..28a8a8d5c5cf2636eea07003a7f594f55b230035 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 9dd493110feae11daf6a9942187ef325ba95fc78..92f08781e2d69acd6fd7a0d8e52c3ceba2ed1417 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 3879abb7bd9c821c86536f8d6d9b8618ffac1643..0b62a315f7bfccf8b06901d303df49c81afbb246 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 21a2a7c81548f8ba57987b857d046a7a7f52ac03..85f10c536ab8a5bddb784cf96edf44be2d46cc85 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 new file mode 100644 index 0000000000000000000000000000000000000000..143c9edae7fb4e1df920724d36be148f48a9b745 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.7.0' +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, '.'), + 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', +] + +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/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 0000000000000000000000000000000000000000..54c1b5525ddd5fc6d9326f9b9b22fadd86534a82 --- /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)$(OPENBLAS_INCLUDE_DIR)/lapacke_utils.h" + endif + +--- OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt.orig ++++ OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt +@@ -454,7 +454,6 @@ set(ZLASRC + zgelqt.f zgelqt3.f zgemlqt.f + zgetsls.f zgeqr.f zlatsqr.f zlamtsqr.f zgemqr.f + zgelq.f zlaswlq.f zlamswlq.f zgemlq.f +- ztplqt.f ztplqt2.f ztpmlqt.f + zhetrd_2stage.f zhetrd_he2hb.f zhetrd_hb2st.F zhb2st_kernels.f + zheevd_2stage.f zheev_2stage.f zheevx_2stage.f zheevr_2stage.f + zhbev_2stage.f zhbevx_2stage.f zhbevd_2stage.f zhegv_2stage.f) +--- OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile.orig ++++ OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile +@@ -464,7 +464,6 @@ ZLASRC = \ + zgelqt.o zgelqt3.o zgemlqt.o \ + zgetsls.o zgeqr.o zlatsqr.o zlamtsqr.o zgemqr.o \ + zgelq.o zlaswlq.o zlamswlq.o zgemlq.o \ +- ztplqt.o ztplqt2.o ztpmlqt.o \ + zhetrd_2stage.o zhetrd_he2hb.o zhetrd_hb2st.o zhb2st_kernels.o \ + zheevd_2stage.o zheev_2stage.o zheevx_2stage.o zheevr_2stage.o \ + zhbev_2stage.o zhbevx_2stage.o zhbevd_2stage.o zhegv_2stage.o diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index bd9785f7ccfd21cf02a4c3c5c86ec1d31218c930..1e915a802ff9bd6829d2c2f8fea22b1f436bfc1a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$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=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index 16af9a124980e5eb3aaebf8dfcb5f1da9a5292fa..30835b6878047a605c1725f908f19b49848f4543 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$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=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index c183debe56adf5d6bd726e9152ab865b81f2de45..b1e3b0dad6fcc61f260595fa264e0f04014d7ca2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$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=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index ba2f665b5bf451880d43b98d6dfa88868829060a..19c2176d82f638eb39abb155dac7a0df68f55b1c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$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=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index dbc806f461f1d6467680cefb0bcc3418b08cd23b..d346fc16be07e1f4240d8bf1c37b08a0ab92633e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$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=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index d0e54d09956161054b0cb278b9c2d72b29996b95..4cb827eecc264a46ed38709f989e425a1dc6eeb4 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$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 f835d278f9cff58e89abe02f361b7800e5ac1ccf..141e1f7cdd8129a8adb690859e17cf6dd258ca72 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 +42,10 @@ dependencies = [ ('GST-plugins-base', '1.6.4'), ] +# 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) + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -52,9 +64,12 @@ 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 ] + + '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-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1495f695f6d4fbe661a710c9b89e234ae62979ec --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -0,0 +1,80 @@ +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/', + # 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'), +] + +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'), +] + +# 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) + +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=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + + ['lib/libippicv.a'] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index b12504dd19f0c5c0cd0cc30ec5e909a5d6cd3e2e..23de8de267aa92e2f9ac0aaa2bb7b5f2aad06db1 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] patches = ['OpenCV-%(version)s_with_IPP.patch'] @@ -35,6 +43,9 @@ dependencies = [ ] preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' +# 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) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -54,9 +65,12 @@ 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 ] + + '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 896ae67a98a2e8d242e0323bb40ae44172f07c17..0b6f2141a73dd22e67a7d5e8314c8a353b523821 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 +44,10 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' +# 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) + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -54,9 +66,12 @@ 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 ] + + '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/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch index d7e72b20c9af2c8a069f13359714a206fc818fe2..1098db34cb84f8efa3585a8f096db06bdfce047f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -4,8 +4,8 @@ # 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 +--- 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 @@ -20,9 +20,21 @@ 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/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 $* diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc ---- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 @@ -42,9 +42,8 @@ # # Please set to the appropriate path if the default is not correct. @@ -36,8 +48,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/ba # export FOAM_INST_DIR=/opt/$WM_PROJECT # export FOAM_INST_DIR=/usr/local/$WM_PROJECT diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL ---- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 @@ -36,37 +36,7 @@ # #------------------------------------------------------------------------------ @@ -77,10 +89,10 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4. +export CGAL_ARCH_PATH=$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 +--- 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 @@ # #------------------------------------------------------------------------------ @@ -98,8 +110,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-vers #------------------------------------------------------------------------------ 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 +--- 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 @@ # #------------------------------------------------------------------------------ @@ -111,8 +123,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4 #------------------------------------------------------------------------------ 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 +--- 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 $MPI_ARCH_PATH/lib64 @@ -124,8 +136,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi OpenFOAM-4.x-version-4.1 export FOAM_MPI=dummy ;; diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-version-4.1/etc/config.sh/paraview ---- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 @@ -41,21 +41,6 @@ ) \ && PATH="$cleaned" @@ -199,8 +211,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-versio 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 +--- 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 @@ # #------------------------------------------------------------------------------ @@ -212,8 +224,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version- #------------------------------------------------------------------------------ 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 +--- 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 @@ -232,8 +244,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-versio *) echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options ---- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 @@ -3,10 +3,8 @@ EXE_INC = \ @@ -247,8 +259,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make - -L$(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 ${LINK_FLAGS} -lrt diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C ---- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 @@ -30,10 +30,11 @@ #include "globalIndex.H" #include "SubField.H" @@ -263,8 +275,8 @@ diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptsc } diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options ---- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +0200 +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +0200 @@ -7,10 +7,8 @@ EXE_INC = \ @@ -277,5 +289,3 @@ diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/o LIB_LIBS = \ - -L$(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 0000000000000000000000000000000000000000..c3f3f806f9fb277ed0eee3b4afbabac85c367d16 --- /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', '5.2.0', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), + ('flex', '2.6.3'), +] + +moduleclass = 'cae' 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 ac26d4212f687dcd9984ba00f094ec6ab2d35089..422607a28b0c4764bc0f85eb70aef4e4cc3e53aa 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-1.10.2-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 3dfb0c023ba40835d21ff111a617aa51c52eb254..26ff9690ecc8fd4b45cea1df9080e6da7fa9f96f 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=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index 274fb15e1f1b1177ebcf56efc4f4bbd7e8e78227..64e4eca3c77c60fdc6a0d26330c32f72de31c634 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -15,7 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$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-1.10.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb index af22c5f5162eb54544e4b5716251d42f8dc95693..ded2f408edbfddcac201caf383f2e884c72b8eac 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=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb index fd6bb36c388a4243691b6754ce1cc9e76edf6050..f7b06dcb04595772a9a564c258f636c1750a76d0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -17,7 +17,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$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/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 23deffc8f49aedb19732a82aea0c0d51bdda155e..ced6423707273fc67e8e83568c18154611582683 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 @@ -10,17 +10,17 @@ 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')] -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=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] # VampirTrace is no longer used : https://www.open-mpi.org/community/lists/announce/2016/07/0085.php libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index aeb2a52e4c0da3c43e51233471f368bd31e00e08..dccf9a16b75916d2f8904d11d79a4f7f5f06c5ba 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -10,17 +10,17 @@ toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # 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 3d626a7c8052893e65a9cbef0eb41bc3c5db7b7f..bc5a7af11f0abe324580db487c4e2b3ce2a66660 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 @@ -10,17 +10,17 @@ 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')] -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 # 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 7d74bf0639a5f5668ee1472b3d894b4f888bf1fe..79bff619c0c0cb1aef8c683e8801424882d0e279 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 @@ -10,17 +10,17 @@ 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')] -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=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..3e05777f37701f2f7d19e7f33af747aac1c54e21 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['886698becc5bea8c151c0af2074b8392'] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$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' 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 0000000000000000000000000000000000000000..b2aa187ae0b4a68a404b6b301bd158de4114db70 --- /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'} + +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')] + +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=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0864ac518d93be7b8eff32f31cea578127e36e0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.1.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['c058052b53d209c7521079e3d2da613b'] + +dependencies = [('hwloc', '1.11.6')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$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' 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 0000000000000000000000000000000000000000..d604042523ea6161775c845374fd529e2556b6cb --- /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/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 0000000000000000000000000000000000000000..783abc638aaf163834ce4bce9beb95a4a6c8919f --- /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' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..81a9ed4ca33fa15a840606b41a484060cb22b5e7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.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': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' 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 0000000000000000000000000000000000000000..489da9288af57bca57108691a308fcb70fc2fe4d --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,51 @@ +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), + ('BLAST', '2.2.26', '-Linux_x86_64', True), +] + +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', +] + +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;'", +] + +moduleclass = 'bio' 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 79% 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 2cbfe2886febcbbb0f562b81f248b74f4c868cbb..b0f832c53aa06e9b82e956031e4c2bafc74e4a0f 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 @@ -1,24 +1,22 @@ -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.""" 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])] +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'] -# 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 79% 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 2fe03116064d8558042da83bea1660ee848cf32e..2f54ba6ec5622136d7235f9422dfb614a2037f2c 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 @@ -1,24 +1,22 @@ -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.""" 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])] +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'] -# 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-2.0.9-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 0000000000000000000000000000000000000000..31aa43dbbad290a69fd78df01a431909d6627261 --- /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 = ['%(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'] + +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' 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 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 b46c6bff0df559bcee258baccb94884dfd406432..807e673a1f64e5770e642d4bd4fccfb74bb7e980 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., @@ -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/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 0000000000000000000000000000000000000000..c6a303fc3e850283496b477d7e5aac13861fe0f5 --- /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.tgz'] + +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' diff --git a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb index c40392b7711f295f9ad46e89c728c0a8e2a580e3..4ba60f4784654bc4969d52d35e8330ccc66256c5 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'), 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 861cd9d963571922fc4b6fd91cac92c71198d1d4..945b858a59d2b33870bb3d9e5fabbcb1eafedde7 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/PCRE/PCRE-8.40-intel-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..136a1027bbbb470d6101d2b27b0cbc5c065769ef --- /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/p/PCRE/PCRE-8.40-intel-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2df6c9ad9001e70b5eea7ef971cee323cbbf1b3 --- /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/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 03cdf3c1c3579232f1288d0911f495a7b3ee51e0..12016d01cbe10b725a5f70d1f37d6a98b3e19b14 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/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 0000000000000000000000000000000000000000..63d0944c2801c8859172e7bdd919ac31abe780fe --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-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': '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'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..33e09a2ad6dc3ed20f784d99f4c549fc7667ec53 --- /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' 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 56139c42c1796d551c735e4fe6beb6cbf07c92b9..f00e26a484c8fd6e940d420d37c91ba42254e45d 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 193d113315c25ffb731d7264eebb623f710dd0b0..deb2a22bc2a27e96bef17c839ad69a011b5fe0fb 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 72b0ef23a93edafacd6a838a1060721b70d327b8..15e5de651c737d8b46b971e9fa6a0c145af10b1e 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/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb new file mode 100644 index 0000000000000000000000000000000000000000..87e4b65750cc408efa1ce685383789971d2148b2 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb @@ -0,0 +1,30 @@ +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 + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +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')] +dependencies = [('HDF5','1.8.18')] + +# 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'] + +configopts = "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +shared_libs = True + +moduleclass = 'numlib' 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 4071bc769afd3a3c1f5bd22b32a1a365602e3414..32e6adc9b7a90a9068057b47b04a760e16b6309f 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" @@ -27,8 +27,9 @@ 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""" +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/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 49864adcd321be1f4c402c2d4fe03662d3bdf02f..099d8a684a6b9d482d39631fce605d5dd4fdb426 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 d3260f31f88f55488164307720bd1b96e40bcda5..4414621a521ecdcf56e381a0d02a3e0452b6e641 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 6589eba972142296011c7f1c7061dfab74410f1a..f9744db69b06f56670aef6e6b278705d56832747 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/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 0000000000000000000000000000000000000000..6502b349fbfb7797179ea41911eedf8bcbf7d1d6 --- /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' 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 0000000000000000000000000000000000000000..fd7e68ba0680269271a6076e2337aba4adfe6269 --- /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' 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 90aea78df70dec7e58a5a7f3a96d5b85deb4d5fd..6ded928e613e22299a404f0c2e1146e5e0e1dcc9 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 312062d04f12b7f722add394ddb02a78d1b780d3..8fca37e015d591a83bf78302d2aa8d5a07e6e8e2 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/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 bb22d3db40840b53c75eb924b164fcc68691e9b6..6d4327f5c0afd9df3a47edc706367715ee18ef73 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 @@ -4,13 +4,13 @@ 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'} 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/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 0000000000000000000000000000000000000000..1454e1f49864d3ac9e7cf6e2c0febde75635a86c --- /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' 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 0000000000000000000000000000000000000000..cefea54afb339468deb7f87b4324a2fd289c0535 --- /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 $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a6e04e3481d3a35f3e5bbc713e543a016766bb70 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1ed42c4139416a64956ef5f4fccfd5878dbe6699 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.3'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7c0ddf0f659acc80690a0bb1fecad7f826d1da2 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-intel-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.3'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$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' 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 1d36878e90c02a9b7bbeb6d08dfbc7897120fa56..261f83dd09ca436fc714c0d859baad042c30bec2 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', @@ -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 fc0341658f6343cf4ccf2b1e0c703af92b02cef7..f2db54990629ba4376beeda8d4769e468a998e16 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', @@ -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/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 0000000000000000000000000000000000000000..7b1bb021f39096d25cff1ed07aec6cad2b458218 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-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': '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' 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 0000000000000000000000000000000000000000..0bd9d6514dc09fed7be0cc973ee5d2c190b0810e --- /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/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 0000000000000000000000000000000000000000..07a9a99e429601b8c609862ff7bc3a39ce894afa --- /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/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 528a6728beb751c89a2b7398a8ba35cf3a680599..33bdd4e669d8896f11ed436bea356fc17841ad7b 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 674a15f04b64c26b4b72531bcce31e143ff8387d..300abe34c8b77516cefae5ccea0c13367cc98fdc 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 c680330c40818f1d9df3b660e4fffa9e72375365..a35b218f7d3b71fb8fb60fb14b751f20ea2959f4 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 288d0bd7ab4b21c1a985d56029a3df5a92a91e9e..6444ef03e078c1c5b705708ab9a2cfb06223b929 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 e65fbf78051b640fe6948da6e099475c2f0bae58..d50c1e4431f1bc1b693a4f180d7756a96ba874fe 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 7be55fa034a338025d55b93959520f3344dd2409..d969aa2c91aaf9294a62d0afea6610bd9e6c7b4d 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 e299f3c676f5c7266a37457cfb83564d792bfe38..c3469f5c4d8380ccdf15d246cc5ceabed2db390c 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' 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 3f257ab0c149bcbc5384f3655c977f5fc4424505..ffd93ce336a8ad2dfa12fa9a71b29f28a0ae9006 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' 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 ed0569f10136967d3595406717d9a1186a9b2438..57e1bb653a9fb511882232171c8786e93d1872f5 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 @@ -29,16 +29,16 @@ 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' # 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/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 79449c632cffd80d62b4f232d4d822076a8a61bf..99940a8a08dcedf8994a91e9c86cff84cfb4133c 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'} @@ -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/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 0000000000000000000000000000000000000000..d9bd112b39d3b7d8966830c695111600ac353b0a --- /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/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 8183de649dd941578a47cde56f936c4b6ef6644f..c1a659916120c02e9755b2c4997c197933053fa4 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 11db9fe0382c98cb7af56913e33f5eb598932354..f11fa30bf52f6f2978b91a9dbae50c30ecaa53bf 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 5223c55c4b4737dfb075318f29b557960be56984..da4fa31fda02d46b525ad261bed7fde7ccce43a8 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 d331f06b60105a6466666ec2886924eeab4a22e5..0becabf5050ad2fc745b42981f9c42b560913d52 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 f4413be29459828872231c11cff8a53292b0508e..36ec81e338c6796b7865167aa59b5163837882f7 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 a32790b7f1ea3548822c3f8367fd5f6359f47abe..e92565e46a5be9ab34e196af724ac4d2cbf6c24f 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 6134d068c99a82a740b9161b8f293786389ac18d..cbbcc0a04ac2530de6da7d4fafb30a60ef3c6aa3 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 c7f412f7697c29ae457d9a9e5f1b3375d854e200..6ed756b3052a9e39c784ad35640f72141967f7e0 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 ebbc3db5a28a98e7cd52bac10ec5910500dff2c1..18b94b44754dfc46253d8f080b3cbc60377b3cc1 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 db08a4e6434729ecd25d8a00ca0c186b9a94c33f..07bf0cde29b303f77e9261295c7e79b346bf951b 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 1521fb5934e8030d1b7e0e397ce7c0f61b8bd808..f8d63fb0671d08b080cf2fdf4b209933ad018963 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 9212c66919f86d27bdd761deefe96f0056bbc8e5..c2177256c30bb20e912c9424fa9071b2f2bdddf7 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 3487dd6842b762b26783108aad40832d056e54de..b323ea3886c6fe0cd81bdd2183345c230cd3c9fa 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 d1d34fb0577a53c7df38e86109ee93af50c5ac35..ddb7b34451a5ab6eca39e3ff646f2a7aa2921b85 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} 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 0000000000000000000000000000000000000000..239bd0fcd43dc901e231b735ead48bac16439526 --- /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/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 c8116fe14fdfacd208bd296115352a67c13d9fa8..4a341a85487a55f5435f341138d2ffb6b5cec8bc 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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb index 2e184fd8019defe06ed7f5a084d06a9a56dab2ea..c862a27b0bb57517800c5b4e628d80ca2689344b 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb @@ -38,7 +38,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..874659978650a1ae66fd23bef5b6642af6666ba8 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.2.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), + ('zlib', '1.2.11'), + ('HDF5', '1.8.18'), + ('Python', '2.7.13'), +] + +builddependencies = [('CMake', '3.8.0')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$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. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' 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 298d4bf94a62c406f6086a78494299b82134af2f..aabbb0dc2439a5650798caed56c847d497d2be94 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 646562570d220047a1e520a1277312c97fc5b21a..f5a5940d0dd87b925c9accd9b2440b8260ebacdd 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/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 a72485e97d248bcb6bbc468027a1e65778ad9a29..161ca2d3837a83ee099a83f038bd42450e0be923 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', ] 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 0000000000000000000000000000000000000000..f39c5f51b0562769daefe05394a9924dded01e27 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -0,0 +1,892 @@ +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'], + }), + 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['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'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.18', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.302037', { + 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['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'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.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-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-3.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-2.01.tar.gz', 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('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': 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['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'], + }), 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'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': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['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'], + }), + ('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 dc1a3cef69a3f9ded529556c250fcaa9c11478ce..47164262e373a4e62a462e2ca4e6e57c32b3b9fe 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 77e0aab0f1306032ff1e441370a12720e669a297..3f4c7638c71f34260cfc8c07ae616d6c286e7fd9 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 087478fa1ff46f1285c7fc2d59b3ec0ad6a6ae3f..8fd86e040fb3f2e2bf27068bd03babe7b9439485 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' 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 0000000000000000000000000000000000000000..7186e3ec910c15c8d54767f0c565d90050a81b88 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -0,0 +1,895 @@ +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] + +# !! 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', + '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', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Simple', '1.302078', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': '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', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['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'], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': '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' diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..edf4ca1f37309f9b8c02fd93f9c8db43d8458f70 --- /dev/null +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.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': 'foss', 'version': '2016b'} + +sources = ['%(version)s.zip'] +source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] + +dependencies = [ + ('HTSlib', '1.2.1') +] + +files_to_copy = [ + (["PileOMeth"], "bin"), +] + +sanity_check_paths = { + 'files': ["bin/PileOMeth"], + 'dirs': [] +} + +moduleclass = 'bio' 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 16cea8d33bff1c5a9fdadaab7d0087a532e2a26b..c3b096e84c3b0af82db9235dfb8bf99c247016e3 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/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 0000000000000000000000000000000000000000..f4cf66d2ef6ea57286d3f0145d65e914b3983944 --- /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' 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 0000000000000000000000000000000000000000..9f45199e957c63f63c862b78cad8290ab3ad82c8 --- /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 $EBROOTHTSLIB")] + +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" +] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb index 9f312bdd69bf415550fa81552a37fb2561557e74..fb465f5c8927a0420b246d8a4a347c5203f5ccc3 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'Platanus' -version = '1.2.4' +version = '1.2.4' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" @@ -20,11 +20,11 @@ sources = ['%(name)s_v%(version)s.tar.gz'] buildopts = 'CXX="$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/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 815c947eaca508729f927c5c81487b4561ec6363..8b0668a68f1606a93d62315d3e6757f49a5729ff 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 9afa456cae7888f16485d3ef0936f3a0e3582a16..6302a94b89cce88229391c3ea0792ed78a7d7acc 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 fca7dea11c2a9f31082fbd373c9eb4c0c6123bd0..c49c4abba6c2b983e56783906a2c882fb4232995 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 a1b0d0ba132ea1bc0e9021233c255bcf924163a6..67556bd5162f78375ed6e19e8fe06897c1d68017 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 = [ 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 0000000000000000000000000000000000000000..537ebb275840f76619b3ec217865ffa59afc1d99 --- /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 0000000000000000000000000000000000000000..9d98aaa67395eb0711f803d8b278e5bad926b4d8 --- /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/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 01c5da8a4821a492709b8a61213b8b5bd9709e33..8261dc989e39cf7707a2f36357a0a5799b92bbfa 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/ProbABEL/ProbABEL-0.5.0.eb b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb index 379bdbc80d26a5bd396b36c4d57679323ad71484..4c23222ada704946a368fa513ca22fcb5a1467c7 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/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 0000000000000000000000000000000000000000..fd93f89fda6ed98d15f3bb73b22b02630226cc7f --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +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/ " +prebuildopts += "--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' 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 1438b0e86a90fcc3dfa1be0ac040288af1f29072..13ffa9e09ba8e14d7024923192c589b2bbf52889 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 new file mode 100644 index 0000000000000000000000000000000000000000..57753b92f3ef8a163a5ce01933d0f6bdb1920b09 --- /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/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 7383e08e6449e7c62c1033673e42c0c0ee8ebd55..4f0ee83679cefdb2cc289bf3247aacf787be1cf6 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 b961fbd0a432bb2a602a59e54bcb5dc2d4c81c0e..56f61040cdc2000b799c7b59e3cd8d7ea296b133 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/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 0000000000000000000000000000000000000000..f8e50daad20abe90266cdc11ea5c5efbd83ab26d --- /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/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 0000000000000000000000000000000000000000..8afd4b1225f1441bb300b374163016696942402b --- /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 += " --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/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 0000000000000000000000000000000000000000..81482a92b26a5524c9e0938a16d0f1e98649e0e2 --- /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/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 0000000000000000000000000000000000000000..fbfabfe34de9a8200bafc0cf68b2db19f835b357 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +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'), + ('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' 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 0000000000000000000000000000000000000000..904febe2a2b393a19b30bc087f0ee8ec5c9da07d --- /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' 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 0000000000000000000000000000000000000000..73b64774073939931b80a6607f51d6206069848e --- /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', '', True), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +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 0000000000000000000000000000000000000000..8a6937f14545e714d711d9127d0127f6d304f82c --- /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' 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 0000000000000000000000000000000000000000..3ee565a8d9b9360a4ed7b956e67d8c8a5e6232e5 --- /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/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 0000000000000000000000000000000000000000..624f14ed188ea0a58a793381768c7c292f1db148 --- /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' 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 e815cc69b5fac246ff483cb8ff33cc5c6798bcee..bbbadf3e32e4e914cb530c237c02cd1d0932bed9 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} @@ -18,7 +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 809068de303a54513a010d973a08f6d7edcf7a51..c5675d814484c3a87004ecc1883d06986afffd38 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} @@ -18,7 +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 c781bfe8b74bc4c9dceb572c6481f7b6c11c95e7..9cb0c165c6b65dfd48fd99ba4b5081c6ea261db7 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} @@ -18,7 +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-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 fd80fddc40f51885bb2f75b08a277357e590e513..492d137f6800987df6f4ac8c0ae03cf03149c065 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} @@ -19,8 +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 6e9aa1f7c47660e47380b7076dd42ab4a25fdf0a..02428a8c5e6dd7958cbc5ccb3da7d297cc1b474d 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} @@ -19,8 +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-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index f325e4238c084f9bbcb9daf528289518580225d8..6b56eb27c33a108d8a3cd858b01af163a32f8203 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')] @@ -90,7 +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 1ba18083e712967aac8c27f4a69400d4d60b3289..8b4e1559a2744ecfa99f17ec3897a3c2f1acabdc 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')] @@ -90,7 +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 e615c893547f7581d6d0ea217240b46b5298f574..acd58a08817e20e55519e6cfe602387da9a08cb8 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')] @@ -89,7 +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 7d445cd6ba97ba7c57b211b7ef67ea2b5e60912e..e8f04d3c24fc9e5db8a8044edc5ecf3a7ea440a2 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')] @@ -90,7 +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 55f10df08f8cecd11049a2dd1f1ce546742abd20..f6fb8098a24c9d1a62fa16a1325704ade6c49276 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')] @@ -90,7 +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 017e1ecaae37816c1851bad94eee84625e6283db..e63f73a086d66b552f20fc7cd5dfa4e260eafcfd 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')] @@ -90,7 +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 276aa8a0f36f3b5512cd64fcca87869f10ab6291..007214e5b0a85f4ab69300d41e0ae648cdeb0366 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')] @@ -89,7 +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 d69b594b089801a7bd59378bb50da618d38a2fda..8a60745ce6c7ca8690b017cb63ef329bf583d509 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} @@ -92,7 +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 ab13993dcf3d948857fd3edf0ea84defe533da8a..f9d52e68ec42ce87b0f0f2d6d69328889dec9803 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} @@ -92,7 +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-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 78953148b07d0b7ce8e840e283640a66e9de5f00..7248257795df4ab4ee882f5f6bdcc6dc99cd8f44 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 c5fe86070e7d3f66c813b221f9a2f4ce09b133de..b14cb9623b6dc240ef76f71b17acf251b3b6cfc9 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')] @@ -89,7 +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 cd19e3b9026c69ba6f6a5e731913f47eb938b85e..161e0d5c72a35c439a0edf2554bc86bcb3d41855 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')] @@ -89,7 +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 917a362739fd79c5678fd76ce1d3fa0bdc8cce76..236dc03eb2b2de9defa39ef96a2541bf641eb068 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')] @@ -92,7 +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 974e57d87ccf7d6bed4132d8b6676c90eb846b24..61b2cea7f16d5859bbf47865744b536fbb634d74 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 @@ -21,11 +21,11 @@ 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 -# 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')] @@ -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 fa2f05cdb99f521fc1e8fead8461872d3c14e45b..15781ef44b5fb081f68ea7ed76e4a2863f8a0ad1 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')] @@ -92,7 +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 914f184b700fba5cf55706ed96bb8eaaf4f052d2..92cc06cd43282c0c957430e7f2fc3bd989a8f009 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')] @@ -92,7 +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 8b707bfd80fa9086066d264a6fea0cc9ec580998..2bcf51b6e34e9a10139d7cfd2444aff315959a50 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')] @@ -94,7 +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 711240b058aa2e3cc29a758de72c54d476383e1a..b4d230688e414a0b2a4291b5512fe5f5c86ceb9e 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')] @@ -92,7 +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 c445811709b702b1a22d832603067c1257a6921a..f016ee6e7a40455262b5dd43c41f7fc6ed08db91 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 @@ -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 ed40bed006921b98e3aecb20bd26f6a7c381c164..7040853aa6e35cde9f24d4dad4681ed10084175a 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 +21,14 @@ 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 @@ -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-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index 62cd674cc5b11902dc649594835e9667c198ba26..01b2892c87ca708a8d4a7c8c765232847e9a299e 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} @@ -21,17 +22,18 @@ 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')] # 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 =[] +exts_list = [] moduleclass = 'lang' 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 ba6ada1467237aadd0d98828506e50c9df09c353..0f7cc1242ba8394020a41d38bea3a89d71fdfb73 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 f39ab1c05674d776d582c462884cdb54b6e8a21c..830570938398b504f7e7badd6485b8715c821b5d 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 new file mode 100644 index 0000000000000000000000000000000000000000..eb4f43f9dda3df0e581bbbc6693e1b775f9c54fe --- /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': ['https://pypi.python.org/packages/source/p/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/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 0000000000000000000000000000000000000000..099f1ae1b247f445ab491653b526b49d8ebbd28b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -0,0 +1,135 @@ +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 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 + ('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/'], + }), + ('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': ['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'], + }), + ('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', '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'], + }), + ('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/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index c93dab2804d6cb744950e58678dedee6163e9b56..b98190bc1bc6b15bd8ccd54bb3e1ae65cb1de57c 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} @@ -19,7 +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')] @@ -78,7 +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 53cdae92ab860f1520daa0dcf5adbc905e1de3d1..6d47c29a417b2fc1ec6ecf8c63409b217a0087b4 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} @@ -19,7 +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')] @@ -78,7 +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 4cd83e24d0f4f969bca9df91ed373f3813d24834..5d62c714b3727e84080b0e48300cc4ae85e5e630 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} @@ -19,7 +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')] @@ -78,7 +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 2608210a179afdb4d3b1bef1a2d58ac585adfda2..466af1fc8338a8f638b0a00a78e3b46fc0f82b0b 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} @@ -19,7 +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')] @@ -76,7 +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 4ffdd56f7800b9dc5fe39837cf155cc71df044b6..9112593773d3b025359640281153e2b9ad0e1e0e 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} @@ -19,7 +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')] @@ -76,7 +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 35bbb975535d761680a4fbeb9aaa492d999190e1..b74b1eef657e2bdfbc2341b1e5bef71a5d671aa9 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} @@ -19,7 +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')] @@ -76,7 +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 d2f51e3f225383ac22796fe0120c29b86eb84b48..fa3597eb0f0cb40b66c998f800b1aef5868b9cbe 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} @@ -20,7 +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')] @@ -79,7 +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 c0ac0d38b167ed567979672a19c5672e53a35e19..74108af01920e13931b32c16e11acfbef6c3b43f 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} @@ -22,7 +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')] @@ -79,7 +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 513384d5b56bc8f6840351d13429524f1ddfafb8..7f83fbbc76d3fcffd43143556e0b1d0b70d28dd4 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} @@ -22,7 +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')] @@ -79,7 +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 95ff34f3f9c16d4f92b6b515b58e529aa605393c..d8028767008e2ed85a28951f1413b7f93be1f523 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} @@ -19,7 +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')] @@ -78,7 +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 055543dc247f6c4468e7ca6846a42848857008e2..8d651bcfebb708ca944d8ec197a8be46803fb5be 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} @@ -22,7 +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')] @@ -81,7 +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 0409f54975348bd1829001623869731240213a96..0ac840f64ed630c9e11fcb8cd5ee6abb0e6e05bb 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} @@ -19,7 +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')] @@ -78,7 +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 2a90fee410794f5472b4c01a1c78db08ab1183f0..8301c629cc8868fbb7de44c5a1be8def0dd9412d 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} @@ -22,7 +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')] @@ -84,7 +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 d975d85c2d94c09a0ea9204032b84d4f49994824..fcb554f5786cb4a23824be5dc263bd08573d22f1 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} @@ -25,7 +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')] @@ -88,7 +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 dca27371ed7ee6aca17c27df12cd50399816331a..d08ab6150584c56c3ccb419ce4889974a80ab175 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} @@ -22,7 +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')] @@ -85,7 +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 a7d56bba1649ef4c244ff86e1dd958201539f86f..3479838d18e8f6731c603339d41f5e57939ef4ba 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} @@ -22,7 +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')] @@ -85,7 +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 6b2fccea289c94605fb2568bf089930788156a6b..e92ff5d69d73492d832abc2fe7b5372fb4ce090d 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} @@ -22,8 +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! @@ -82,7 +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-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb index 92748077e8fa6a40c10130748bba83351a0dd22d..b60dac883260b80b508d2552e05cda1bb12c54e6 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} @@ -17,8 +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-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index 2c98486b9278bd013e550fc5097f3dbf4141222b..0f597d584c8708addc110f8149f0765ba0cc4972 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'] @@ -42,7 +44,7 @@ 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, { @@ -85,7 +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-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb index f7679002a18e7975cfa4c1ceb0c954ab1b18a3e9..8249b3b9b94794be8ea8240e9579c1712b632a97 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} @@ -17,8 +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.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index 23449c08344b745ab07671f6003efe17ff6cbdca..2963dc2fc79f36df8a851feb3f3bbf2215d4c887 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'] @@ -42,7 +44,7 @@ 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, { @@ -85,7 +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-GCC-4.8.4-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb index c83dff187b29fb8cd1c5af5288e12872b6480914..7040f073ac074e96f8b3af96db927f671038d290 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} @@ -19,8 +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-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index a2e4addace20b764cda53531311ae544a52539bd..4492ecb9d73cdac455e1c7b76c30194189ca471a 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} @@ -19,8 +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 5ca1dda84ebf4921cc24b0bb1e3ecf64c7d3da76..6953cb6dbeaec42403fbf5f08193126f15319f98 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} @@ -21,8 +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')] @@ -85,7 +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-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index e9063410dfeec2b3c5d8c206c2e47b6735d06fe9..ed68c4c30474de74673ab38b29f02dfe2a259889 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} @@ -19,8 +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 b636f6b2ef65feaf08d11a7020afa201bb16d9dc..0f287711fc0ccd4832f7be98aef21cfe3bad4f21 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} @@ -21,8 +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')] @@ -85,7 +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 82282d02d9c59b7288f88b1ce95ff78f21429ccf..77b75dd24234b70008f5cf9dae60e08bb9088b94 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} @@ -21,8 +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')] @@ -85,7 +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-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index c78274679f6a502ace6591f31b60967423a4895c..1ef84a7f5fbdb1726854030161194876bae11801 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} @@ -18,8 +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 987f0852f63aeadfb8be7fa65388f8638c396336..3ba0f79c58714e2e05ee9cc0bf703deb65c0d414 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} @@ -21,8 +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')] @@ -85,7 +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 37abf12093b638069fb0196b2261d71c61207510..58ac4915cc03a4d6eb2425850b9f80c08eaf50b5 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} @@ -21,8 +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')] @@ -85,7 +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 7bdd55756a3bea354c50eb16cead6dc8314a6128..f324c5da55596b358e7e308a9cd53bdc8b6c3d48 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} @@ -21,8 +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')] @@ -85,7 +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-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index c672a429fd7839f1081602d1c9aa0105c75aefbd..ca9022ba60b6e7475035b17458078bf2d70d19aa 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} @@ -19,8 +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 24081c5cf8cd659ccc7f85ef90ab0dc64dc1c0e8..76e8491a9bffa02fad0f15fda3d67b5f81f92433 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} @@ -21,8 +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')] @@ -86,7 +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 fc5033662d8a96ec9887f5b14c299ec6a7fbbad3..e15e16e66c1e6a1b9f46482f3cc9741a7b2d46a5 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} @@ -19,7 +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')] @@ -59,7 +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 1fe945390aa2e1dd00c7315e29103136c803670a..fbcadd2903b9decb0d72232c79da170db955ee8e 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} @@ -19,7 +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')] @@ -59,7 +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-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 0dc65b97cafb45b9b359fe8d356bd8ac1cd77765..d79d72ab009dcf77c515b4a6b2a8b3a77ebc17bd 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} @@ -19,7 +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 97e6c04ce768b4701ae26d6d4780bdc15cf123ee..cacde6a1791ba3460834d653bfa533bb18056380 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} @@ -21,7 +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 ba9c2f40b215f23b21e3e540c5788b9642ac80e3..aaa2d02a7e53caecf41a6c62d7ea5f0f84396639 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} @@ -22,7 +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')] @@ -90,7 +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 910cb21e5cf0a7003b352fee17cfbc94d01fa9c5..80c176feab09d14ea6e1aaace30567fcc95e7775 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} @@ -22,7 +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')] @@ -90,7 +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 8f08cf73e46a4cf26573fed8045f552886a425ed..e220cd9cc432dc8311bd9abfb4efb850d45750f7 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} @@ -19,8 +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')] @@ -89,7 +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 825c8e6b10acc1a20d3bd1204053a834129f1d6e..1fe2eb47485cfa5564b159cff46b7150b2336a1e 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} @@ -22,8 +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')] @@ -91,7 +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 new file mode 100644 index 0000000000000000000000000000000000000000..3794d8056b5c06666223b0440e09cbfb5f4b15c0 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -0,0 +1,128 @@ +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 = '1.10.4' +scipyversion = '0.17.0' + +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'), # this requires a full X11 stack + ('GMP', '6.1.0'), + ('XZ', '5.2.2'), + # 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')] + +# 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': ['https://pypi.python.org/packages/source/C/Cython/'], + }), + ('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': ['https://pypi.python.org/packages/source/p/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'], + }), + ('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' 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 129c326cbbd9b44389316069cf5ac5a2ad3940ad..0ea37fde6ea6e6e32f269d1d34db2866cc7388ed 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} @@ -23,8 +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')] @@ -91,14 +93,14 @@ 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/'], }), ('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/'], }), @@ -111,6 +113,16 @@ 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' 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 395e40515b102c6def7ff6326907eafd508bc59d..6b27ddc007fcb0e239053595176ba33223d1a418 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} @@ -23,8 +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')] @@ -95,14 +97,14 @@ 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/'], }), ('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-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index f49b2ff08519ec0a3549129deefd04a9d163b443..0f528e01582f89fdc32756dd4fbb99bdd550acdb 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')] @@ -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 f40c4aab551a331325e3f14f233d4673bd4a6ae4..2fc712658f2403d084b1a641b0cd621ec9f2878c 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 805061ab30b31af53ad2e6564cfa0550060d6e4f..198569f10b58edbfe02e0f5f4486902b23649834 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/'], 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 0000000000000000000000000000000000000000..b226f52d5171ed4f2a0e3c0013ff535d1a306158 --- /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' 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 0000000000000000000000000000000000000000..3d09924f96668c7593a0519223e4abfc6f8fbca2 --- /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/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 0000000000000000000000000000000000000000..d128f00a0791d34b1bde3afd5b2f00c924187618 --- /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/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 0000000000000000000000000000000000000000..85d32100c57358dfdd909486fee48cc18d74d6e6 --- /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/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 67abbe4783f69e09f877beeb250d3fb4e5d6f040..ba44c00e4e78b4430279dc20c290ae48195945cf 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 9fdde707312cba290df8d7ee6d6e6de93edebf2d..bead17f746237f8ae906da2f117dc1d10c54eedc 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/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb index c89d3af9f2898475e971cf1fecf04ac52cf3ccc7..cc1d205d402f6f9feb304f256ac9647a2b0a1cd3 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')] 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 0387cd385f720012a4a2e64e4085bf23ebb7ac0d..f2d716e0cd57c932e7a6f92c60edb9116d52d413 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 50d6cb2145c31cc0367c6cd648728b4b2721c53e..d31fcf86b6a455d61aef4057573e085681874547 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/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb index 8d5302dd6c83b5b456b349eac2d04efb40e1e2e2..f72f7b4c0ec21e2f65586da6f81efd72cb6ab137 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/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 742c2507d142c5853b4d25b53dd708d5ec1157aa..1d6200df1a145011905445cb43da485bb33e30d9 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 $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb index 88bda5b21fd6d1f7a723709094b83329177b9596..80d1371c6d970b0ebf7fff1a74591a0aa6c0e986 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -15,6 +15,6 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb index 9ac838302496c32bdafd1c7cebf9e759da69bfc7..c0f8364e0a9d8bc641d7c70a0cd2ed2d3cc46215 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_112')] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb index b7bb2304d457885752499862b29e5d4bd4304bd7..0e3b39959177004a5bbc22b6911b4a8438587379 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -13,6 +13,6 @@ sources = ['%(name)s-tools-%(version)s.zip'] dependencies = [('Java', '1.8.0_74')] -modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/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 292fb226d32d2adcf50372464bf0a88e70c5928e..b6ccc91bd2510359c93332b87b5bd7384bbe5a4d 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 770c70dd5f7fca5b595374c442ef1c2a42b2472c..e3e7f189b133c2886de6ebf4d5a15c56d8d9c3d7 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 e95cb85cb9fc0be28fbae6ad68496752d5a96775..a50f50774ee6e71c62e5aa40a1422aa66000ed20 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/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 0000000000000000000000000000000000000000..77fa36d059eb6d6c082bb65666350cdc9bc45fa3 --- /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/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 0000000000000000000000000000000000000000..185ce92b1dc50d965269d5451361c908c2ac17d0 --- /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' 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 0000000000000000000000000000000000000000..9306c638055f25cfa7f59a70b73a5fdf4f6ea4b8 --- /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' 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 0000000000000000000000000000000000000000..dadba07804cc2e118b4dcdbed779287c3213cbb6 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -0,0 +1,35 @@ +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', +] + +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/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 0000000000000000000000000000000000000000..ab1875711a9285761f82a4c0662feea4ad193415 --- /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' 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 0000000000000000000000000000000000000000..b3ddd790cb307dfc09b1eafaef1f09762fd4d5ca --- /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-intel-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..25371013ebe07e3a018eb8b9435f2f95a37aade4 --- /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' 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 0000000000000000000000000000000000000000..a83002f30da6958f417d4728f582398343f8b555 --- /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 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 0000000000000000000000000000000000000000..b75a0d85ea9d6b7e280c79b9f49f6ad273a90c02 --- /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/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 0000000000000000000000000000000000000000..90af56a5b1a75269862383cdd7d8d5acce1bdf6d --- /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/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 0000000000000000000000000000000000000000..0df86ffc843481a8bc706277aac614bb44be26f8 --- /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' 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 a9b5ed1e232531cedceba2574a6dad033864f94e..e50c9d60b6ebe1c5fcb56d7f849436b0a76fa4bc 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/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 0000000000000000000000000000000000000000..035c739fdd7a2d2d9370d6806201186a29f10cd5 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +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' 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 fe4231de3be298e8bb2000592bd12d0fb8eb1105..4c956fc8b126c2ab9694155400872442fb19ccf7 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 4b1aefd0e6d20baec80e5283086b752ed62c218a..83eb4807ee817ca93a0dce84d270ab665bda5784 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 new file mode 100644 index 0000000000000000000000000000000000000000..7ba652badddb1849dd7ba89e366e125dd43be882 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,34 @@ +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/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 a4fd060e9c31ef79e696908b3e1e2b0b0ddd860d..dc44707f0f8fe74bda8d0cfc42f27ca1174ef6f5 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 6c89475fe0bc1ce19f8c2efbb6b497691e15c2dd..1e7549ab87f42ffbacfc4930b697ff282accdd96 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'} 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 3deb45334a2f85f8443163e0b58018d33a49bbfb..3027748d68f019e6430a9e98c0aaf1e4abae4ac0 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.""" @@ -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 64b04ec53c33de2b066e44ce7ae2b22d0076a4d9..fb8104961b4ff859f187f92876fb55b26391c09c 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.""" @@ -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 new file mode 100644 index 0000000000000000000000000000000000000000..1f800a9ecbb8a14c92bd8cca1075f9a1953a72d8 --- /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 0000000000000000000000000000000000000000..14ca3145051696b19a1ca109c16fa363e51ff9aa --- /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-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 0000000000000000000000000000000000000000..fd34141ef944073bd0fb7ae341b8322ab116f22e --- /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/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 0000000000000000000000000000000000000000..51988758fddab24c556046c0418ebcef649deca4 --- /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-2.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb index e9345ea16d747348719cb2a461ea06b32e669fe0..3c5b16c424df9f925fb9d7ea4534cca6d0d3dc02 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 56627b2c07ddb222c1be024ad477ddf1d62a2d0d..3dff68438ef66311a7c2b0c88b6c139ca679bac3 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 7a7091bb5e2671b5b4004e7cb4e140ec46d804ba..03255276d8ab971fa05088d32c2112c17c313612 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'], 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 14ba425f1fd6f47f11fa6dc44dc3a4a3eb6675eb..d684c53f55a64c0a832a0076f8951c83ab661b92 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-foss-2016b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb new file mode 100755 index 0000000000000000000000000000000000000000..f6b756484fb8bc4863671186a9ddfb4a92d2dd73 --- /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/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 0000000000000000000000000000000000000000..224169f86e5b4f18a90c9c1815f9a4cb5f8723c3 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-intel-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': 'intel', '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/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 65a73afe7df4b82ac028ab13111d788786832470..147a4add747887fc08ee5e984ce7741950e3630f 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 b69d0d92ddccf8c0bbdf11f201c49c19bf7b3da9..0b3259fa6d925a1cccf1025bb0ff13f2cb3cb72e 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 7da1e4a7f7181be6c837d49db84c243690fe24fb..af331b28c2cd24d249e1439a7c2d8337a8c14c1c 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 13b9a47c545bc7b49554c2ab114d1a44a4ce7da4..fc283ffce3f5b6b327eb871b5c2ba7aa4569f98d 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': [], } 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 59517cb97857238994bf4e5742780ddfedde5539..86cd99461014abc6297337da1c6f0217d26c67d5 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/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 0000000000000000000000000000000000000000..948a2bd8f6458665d504d0262bb664490fdb01c3 --- /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 0000000000000000000000000000000000000000..3ac0511ce13895fdbe27603cd4cf68f65035e85b --- /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' 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 908370bc3a1e18f11f9cd6d9eac0f912d7762334..3e9cb1c1a3116969a14e57064f6708badad5bd9c 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'), @@ -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/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 bf649cda81c20497028cda994d98f1ee73e4efe5..8ab67d6ce02cf9ac26725de2f30d2a9e1deebaed 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'), @@ -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/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 0000000000000000000000000000000000000000..7c6022d3f6af241c1742b159ebe8b1236089e85c --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +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'} + +dependencies = [ + ('Python', '2.7.13'), + ('pymatgen', '4.7.3', versionsuffix), +] + +# this is a bundle of Python packages +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/'], + }), +] + +# 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'] +} + +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 0000000000000000000000000000000000000000..86166ed4e44388df25c6b2ea3a4b9c3fb6d83534 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +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'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('matplotlib', '2.0.0', versionsuffix), + ('spglib-python', '1.9.9.38', versionsuffix), +] + +# this is a bundle of Python packages +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/'], + }), + ('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 +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' 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 695617390c7ef20fd3803cdda85cf7fc1ec7e7b5..8ebd6c8d2ebe9d185393b65c1a0bd386899af125 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 98760a6c19b4b09008b9954f63970153a95996c8..b72f894f40d16924a8bfd802027d25296345bf5c 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 9f1bdc61f3a6aa1e81472f711562588181fd3a29..1f3dfbd69d054afc50b8d075ca45e3ac9490de55 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/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 0000000000000000000000000000000000000000..73895f04cbdd7851f7efc71d08be73f2cd471cb9 --- /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' 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 0000000000000000000000000000000000000000..4a946468909bd74a6d1834760baef0508c7993b5 --- /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' 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 0000000000000000000000000000000000000000..2b7816fd3c8ec1cc1d3a558397b6f2e34b7a4aa9 --- /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' 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 0000000000000000000000000000000000000000..4878b7d6294548cb4e540ae22e31237e6cd1fb74 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,58 @@ +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-%(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'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), +] +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-2.14.12_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch new file mode 100644 index 0000000000000000000000000000000000000000..2eb3299a7d32e75f4c7af42db1a79b6ba4159f02 --- /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 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..837899aa93c0bfc02bdc6cae639ad3afe6dfe658 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.18.4' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$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 0000000000000000000000000000000000000000..5d04066fb19822e0f69bb40d8ee1a35174446adc --- /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) 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 0000000000000000000000000000000000000000..4b9209b380904fa4a0cb8ef8b53fdf998dfee09c --- /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' + +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 = "%(namelower)s=%(version)s matplotlib=1.4.3 mock nose" +channels = ['bioconda', 'conda-forge'] + +builddependencies = [('Anaconda2', '4.2.0')] + +sanity_check_paths = { + 'files': ['bin/print_qiime_config.py'], + 'dirs': ['lib/python2.7/site-packages/qiime'] +} + +sanity_check_commands = ['print_qiime_config.py -t'] + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..32b23291118295f89127b71b49a9c1163ef5a114 --- /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' 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 0000000000000000000000000000000000000000..44efa4db59cadee54a958082b2511524d065b835 --- /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' 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 0000000000000000000000000000000000000000..13dd45e4893631fa0862f139885b1cea020d5d01 --- /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-2.10-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 0000000000000000000000000000000000000000..a974a1c6aca779eed595e72b704a0d7f21084f73 --- /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 0000000000000000000000000000000000000000..cca6cde624560b33d85656c6fb6b4a77e86c46db --- /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-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 0000000000000000000000000000000000000000..f6edee2ee2b680a3b153d70742fcf2a3ccfaa936 --- /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' 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 0000000000000000000000000000000000000000..e3f0cde60024ef36e4f4a946d0a939095cf7c0a6 --- /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 0000000000000000000000000000000000000000..3abd6f5965f7915aef2574c632fb911edd191f0b --- /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/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 53f43a015db96fdf837b574ffa698248ce8fe6d4..0aa79c308343bf7b1c121404dd42788ec3fb49db 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 diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index eacf9a8384c836d3e7cd441341fa27f762a3d460..48881e75e80e29b1787463f4ac715da1f945d454 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/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 0000000000000000000000000000000000000000..f9818f430a7ff8afab6b27138998af047ba519c4 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -0,0 +1,29 @@ +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'} +toolchainopts = {'cstd': 'gnu++98'} + +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' 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 0000000000000000000000000000000000000000..1fd587b6e305f755c37f112a21d2dd6401c7a56f --- /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 0000000000000000000000000000000000000000..43f7c73fcc7f48ae69bd93ae362868d03d2d227d --- /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' 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 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 0000000000000000000000000000000000000000..a05afd509676b8f21db2d1d68fe5945927c5d760 --- /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' 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 0000000000000000000000000000000000000000..ab4ae0dab890d73a8b15f7167d4b35f68705376d --- /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'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' 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 0000000000000000000000000000000000000000..703fb053f6bf6dc5bbed340bb6add71701d96427 --- /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' 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 57849d2efa21f0c22e9fd5acd09fa19afe1ea6f7..f15e4b6ae50adbe3834f888aae913681872cc6f1 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', @@ -21,33 +21,33 @@ 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 - '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. 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 ' @@ -55,4 +55,3 @@ buildopts = 'all tddfpt neb xspectra ph ' parallel = 1 moduleclass = 'chem' - 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 0000000000000000000000000000000000000000..4a105c34ef98af9662832c032f030a9fe5e95562 --- /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' 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 0000000000000000000000000000000000000000..0de53d6790a012bab079d03e6fc9f523ad0ad011 --- /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/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 0000000000000000000000000000000000000000..f2b00bf19240418170186aa65d4c947624c6ac39 --- /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/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 0000000000000000000000000000000000000000..a477b16bef63dda6bbe65f0fb69f8ec9dc59f051 --- /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-foss-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf12b1ad5e6de500b48657528df36efc4f2d0ca1 --- /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' 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 0000000000000000000000000000000000000000..4b8e6389edd49c1f7a45671108542ab3b9485513 --- /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@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' 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 0000000000000000000000000000000000000000..e88f9455e66a3873659c0a190cbe620af342b002 --- /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-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 b12bc8e75dd03e5b2cd43aa85e88893d53fdcca7..fddd66f795751c639a61dcd4b46a1f1a042bd7b3 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 561a883aa500b17e9c741000178385520addb4f7..41c4f5301ff830d6f76b7fcf2d9cb904a541aff8 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 d58882331fbc921f830f0c3d73f012b8b1d5e7ee..69f1781b6910f02e8578a4944eba68917e67ab5d 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 8ba729ce15a2d0ba5e6c857b2a853b28432aa252..69437c1b5a80e5012ed0c3cf48f618518c847606 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 e96756b81d78bcea0319b335b3cc7f7803bd5a24..99f0a85afdff339d2c196808cc6b24b12b32a413 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 86f63c2452bc02bbdeb63d281cd155027f33ad3b..b6f9488dc0a25859fced88b547b6bfaad0e14013 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 a7f037b0a775d438d8489f10445ae9f8ede50e79..6da04393a83d55b9eebe68bde4b3778f1b6eb4a1 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 c79a8bd4e82de14e33e02d94dc88c757851d3734..25ba222aa635c8706ce9ce80772269e8e90053f0 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 3c069b9b81e3361e63488de2b7a655a12364b9d9..8abe6d999a1076e902c3702bdf42e7ec8e0d5ae9 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 8d427ebb5dd175b6f4c1ade3ea644da7577763c4..d3eaca313f631ccd6d57bbf6f957d820a351aa37 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 b2aa05899780218aae3e7150d360895c065804dd..f34e0f18e65e1f1eeb615354009da663acc822c1 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 ee87a80c866706bc2fb264641fac3fd34040ec64..1572f6e35f3ae386525c8718fa41448956b34bee 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 31222cc1f7cb04d4daef9b7728fb4704f7c20c0f..b0d2830c75a7de5693fafc075eb35f3168c566a0 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 866b40ba8180c1e122242c636fa082869de58253..a2eabbbdcd126b5bc65f1623d7b94d114f801ba4 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', 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 499d383ce4fc67899016e9947a2dba34495f0130..ab47b2f1325ac9f6e6f39d29b5f1e58ff05578b0 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/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index b54b0f68e9b75c468b2aee4e5825e1f215ba0e4e..95846046fcc051f4504e33074a0a1a376f45e9a2 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 580f74438d2ce591213dd88b066ded2a05049aa8..1389b272dd97610f9d897163d28214e040eeb527 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 004c178582be56e6841d2bfbf8f2992141629f95..0acfcbd0b3ca6e2ab295021d15c9a3702729638e 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 1a886a00c96e84d063a6b2cbd8d934ee6c2540c4..39a19900bb04cb652dc872fc6352d0d8645efea2 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 7baa761be0155d372ce09e1a5326058207687901..ad907eaa040750b6ed346a9338f3ae05a7e45ece 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 9e8837b860fcceaf6d9e1330131e07eac9b26116..7c7e501aad8797ca3f0f6529a97d6db4a412195c 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 @@ -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 ea4614f23dd286995def2626768fed1c6bba17dc..9380aadc9bdf80e3c7c301cb70555d9839f30705 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 @@ -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 21471e59851c2251e434818f4d0c4d92ceed55bc..88223934d1faba744b5c7495dc0f9222a555ea71 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 @@ -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-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb new file mode 100644 index 0000000000000000000000000000000000000000..3b6ee9a746b8dc2cd3e374c2bbb649a152a4a8d5 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -0,0 +1,510 @@ +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', 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', 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('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), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', ext_options), +] + +moduleclass = 'lang' + 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 new file mode 100644 index 0000000000000000000000000000000000000000..963e0745721f5aec823bf5f7ee52c9f20f6a334b --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -0,0 +1,511 @@ +name = 'R' +version = '3.3.3' +x11ver = '20170314' +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 + ('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'), +] + +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', 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), + ('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', 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), + ('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', 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), + ('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', 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), + ('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', 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), + ('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), + ('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-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch new file mode 100644 index 0000000000000000000000000000000000000000..829b1123424ed5690c9e8d3d6a89b1709e2f81d8 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -0,0 +1,301 @@ +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) +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@ $(RCPP_LDFLAGS) + ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch new file mode 100644 index 0000000000000000000000000000000000000000..660089c7d5ea37f820aa528fc38776c722b824cd --- /dev/null +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -0,0 +1,14 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- multicool/MD5.orig 2017-04-01 21:30:37.105382230 +0200 ++++ multicool/MD5 2017-04-01 21:30:30.095337987 +0200 +@@ -20,3 +20,4 @@ + b18b7e9e5912cf1014aa2c2fa8e86047 *src/compositions.cpp + 994ea793adf2455b973554d9b8dacd99 *src/multicool.cpp + 8e6ea24037e92ec9c30f699f4e3f9b8a *src/multinomial.h ++b1d3a4d02405fe08c7983c479bc27f13 */src/Makevars +--- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 ++++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 +@@ -0,0 +1,2 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb index 985c8834410dee1a0007ae834275701ae6b5df5b..1eb4b3b8468ff3b8ec5eda47a5979993bf9ef6fe 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb index e09f71abf5311cc945fff303141937988b4aef46..7004dce41e20592936f90506b299f5315ec106a7 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb index 0fe0530f3ac458336b7b01ef6ded89cdce9fb398..d7300ce6e9c5296cc8203307240d9c6bc1712d29 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb index af08c5c5e5b419e36c2137e17d3987365ba25866..ee4a21ba9325b5f829d8039cb16a8b5b732f49fa 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb index 0868a2b38e16acace4b0a5184109d6e666ae026b..fe4066ef14f76e018ebca06f1cec60c9c5010deb 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb index 3a1597463cd48a11bf4bbb1a7d07c07182f4938b..fbae2547b276a814bbc6e99ffa4d1d27a45459b6 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb index 153acb74247887356d41d67914a02a1496bc2df6..c9087e258fd7c247d38d863ade3e8bbb94cc29d2 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb index e7ee2daf46667ff343bd152f4d941b51d342a35a..fdc9f9754463fb533cb77d57b3710fd1e0ddbfbc 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb index d053b3dc21b0d5e455c1541b6662bcd38a0733ec..1c1435652ce03da7c719185740e837a69a1d8472 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb index 575001db8dcb37ae2efc8a459e9dae31cafd59ea..0ccbb936e89edda990f451761f09acf34fce4bab 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb index a1fec5b741523f28b4375727b8b4fb2bf336e68b..dc772a459ba164f8b0948abce8bda036eb6f4ab6 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb index f253cc9c29a0153bf864d5d4e9ce818751092cd3..caffbdd4c7f7e463ee6f1051c4cfce5b40bed855 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb index 7eb0b37f64a98ff06d547dc2dcab9e6381d4803a..05f29e6aa62c9b9fbbc61342c642568bb06d9833 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb index 0058765fc566fe88bd8c5a8016197c9e20a0d4ed..25dd91ac1dd36d7d4d65656a58914bee54525718 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb index 86dab359ac168b915f49b5289e345fc062466847..eef4968327af5eee36684e9b194b72e6b1318176 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb index b107d2a11a0fdd0fbe5c5b970963067d78112421..89cf1e0f0bf82eb13feb24d32287a45748a0b8ec 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$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"], 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 0000000000000000000000000000000000000000..4ff67a0efb6d4f3a1f758a9a13bb34e204f97039 --- /dev/null +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb @@ -0,0 +1,23 @@ +# 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 = {'cstd': 'gnu89', 'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/~wash/%(name)s'] + +sanity_check_paths = { + 'files': ['bin/RNAz'], + 'dirs': [] +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..d772d057cf840b3f2fb6089dbe0a800a0657571b --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,61 @@ +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': '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 = [ + ('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', '5.24.1'), +] + +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)", + # 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", +] + +sanity_check_paths = { + 'files': ['bin/add_rmgAmpPhs', 'bin/getorb', 'bin/make_raw.pl', 'bin/make_raw_alos.pl', 'bin/roi'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'bin'} +modextravars = { + 'INT_BIN': '%(installdir)s/bin', + 'INT_SCR': '%(installdir)s/bin', + 'MY_BIN': '%(installdir)s/bin', + 'ROI_PAC': '%(installdir)s', +} + +modloadmsg = "These environment variables should be defined: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch new file mode 100644 index 0000000000000000000000000000000000000000..f9b938a005312c2e1bb35137418a813cf658c9e2 --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch @@ -0,0 +1,15 @@ +fix bug in ROI_PAC v3.0.1, cfr. http://roipac.org/cgi-bin/moin.cgi/Patches +--- ./ROI_PAC/intsim/IntSim.f.orig 2017-03-30 10:35:09.702908447 +0200 ++++ ./ROI_PAC/intsim/IntSim.f 2017-03-30 10:36:32.204116436 +0200 +@@ -1339,6 +1339,11 @@ + ntotlonpx = ntotcpx + endif + ++! update these after padding has been applied EJF 2013/5/9 ++ nslatpx = int(dem_pixel_min(1)) ++ nslonpx = int(dem_pixel_min(2)) ++ nlatpx = nint(dem_pixel_max(1)) - nslatpx + 1 ++ nlonpx = nint(dem_pixel_max(2)) - nslonpx + 1 + + write (*,*) + write (*,*) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb old mode 100755 new mode 100644 index 9a78780f34e26d9309cc5305250f7ad203b3eba6..b3d257608f184f8444ed674dc3dd8da75f322e87 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['e60d1a896299d000b6a34f032debc9aa'] python = 'Python' pyver = '2.7.5' @@ -32,4 +33,8 @@ configopts += ' --with-fftw3-incdir=$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' 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 4e14ff0190bb88af2cd54be20f320bdba0c80f7a..99a4b3d8d69a5adcdf0f4d1ad5399b371d74717e 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' @@ -32,4 +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' 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 a65a7332782025aeb8d5e3c97c0146c9a0a81c6e..c111bdfea0b3f33dc0e7fe16ae32e9d9aa7d7dae 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', @@ -36,4 +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' 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 e025c77b0277d5835714260a9d4b8acfd594c77e..a90994c1ab810703a33158672382f81c109bf275 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', @@ -36,4 +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' 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 cc50539ec7d09cd80d6dfcec20518e34d41fc165..f662b0dedadff893f503ee76d5e6586b91054d49 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', @@ -24,7 +26,7 @@ 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), ] @@ -40,4 +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' 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 05baffbd1658d53e4c159d201a0f0bc0d65f70ed..6073d0e56c310bc0368f092e58c031c82ab7fd5f 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', @@ -54,4 +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=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb index eb76e73818f0549707831fe68f0e32496bdb0a4f..80a084ac4d7a25105e19d526d252b5b4f3abf452 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['fd9ee9cfc85cdad3d7c2c41a28796c24'] + patches = [ 'configure_FftwFromMkl_28.patch', ] @@ -34,4 +36,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index fc6f18713c5b439b46c0eafb5fd7efeedc035fda..718fb2f36dfc341da8207b641f337d8d868fadda 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['fd9ee9cfc85cdad3d7c2c41a28796c24'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', @@ -52,4 +54,8 @@ configopts += ' --with-x11-libdir=$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' 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 7d1106317bf4dd1f00f68fe0e33eccc22497579d..d8466b4858e718d694b50caa207da6f067dda40c 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', @@ -52,4 +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=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d3d2000b82fa55046cdcc55b8636efc8beca98e --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,59 @@ +name = 'ROOT' +version = 'v6.06.02' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.3'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), + ('CFITSIO', '3.41'), + ('freetype', '2.6.5'), + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('GL2PS', '1.3.9'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$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' + +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + +moduleclass = 'data' 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 81755cd85648e0302e3b4db8db8bd074be690fda..902a9ecafd8c2e1b8b04d0050a948d2633e1f6e1 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 +42,8 @@ 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' 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 e773ad310a37ccef695734d22fe6011d31e6f358..f0918866798e4c3d01a057c451a7dd8b219be6c4 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 5420a22996be198b95a6a16494b0f93c3f8d0fea..85267f0972423a7365e4ce99dab425d5f94841fa 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 d01f2f908948cd3c54b3e29a9436d6fbddecda34..e70842c9f5b0a3cc77b80b6e6ed5ea50ef696670 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'], } 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 0000000000000000000000000000000000000000..8d81791c83b2438bc587250a5171c0ce23c2ec46 --- /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/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 506890dce28fea86bceb7244e506c77f0584270b..462568a58d3b25191947132fb3f6dda27970aa92 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' 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 0000000000000000000000000000000000000000..fc07069bfffcd51840368ac627945f039af9f067 --- /dev/null +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -0,0 +1,30 @@ +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-%(version)s.tgz"] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%(version)s'] + +dependencies = [ + ('netCDF-C++', '4.2'), + ('Boost', '1.60.0'), +] + +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 ], + 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], +} + +moduleclass = 'bio' 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 10b2a8fd9cf6106fa3492a12934a14b6af9c7b84..64d1ea29a24d2ae49e0a52c7130061c4ff25947c 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': '$root/database', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb index 86250d9275bb021104f14638157113a877ea0ca7..d65a2614d96bb3327ffcfe43f40e581893932043 100644 --- a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb @@ -13,8 +13,4 @@ sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] builddependencies = [('SCons', '2.4.1', '-Python-2.7.11')] -modextravars = { - 'ROSETTA3_DB': '$root/database', -} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.46.59086-foss-2016b.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.46.59086-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ccf154c6cb35af90529108d8690d7591d43b7fd6 --- /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' 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 dc1928028ee8ed6ed233f735c488dd6d2789cddd..00858b739e4560780ca370ec98c7d5c1f4623ebc 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' 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 de615e762046ffe34e4e7caaa5df4b9a0703f9a0..04ee893a0e3de6ac2ec8f85be742e44fe2b789a8 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 a06ae545970e984f20cca5d3cae9c30b2009edf5..ed54478e03d9a8d51a1eac902c42700aba586f52 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/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 e5d10e806149d54f1907953ff14f3d3142c6147b..ebe8bfa5d5bff0f3fc1abbdda886124d3b5f9ec0 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': [], 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 0000000000000000000000000000000000000000..9858d484473c8f9b8f64bcbe45db4f3acc706576 --- /dev/null +++ b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb @@ -0,0 +1,30 @@ +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 + +# 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 && " + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [(['randfold'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/randfold'], + 'dirs': [], +} + +moduleclass = 'bio' 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 0000000000000000000000000000000000000000..2546a92787a36622e1b91ffde015fa02d5cbaa49 --- /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 0000000000000000000000000000000000000000..3d08d7d724bceb15d0997b0e84048e05da2ec910 --- /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' 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 0000000000000000000000000000000000000000..efecae95e82d8260c65c1986d29df209d6518378 --- /dev/null +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +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', versionsuffix + '-freetype-2.6.3') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' 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 ec3e8a22d530f33f91e242fcf1ecd7a1021519b4..631b1a8562e7e0722e1a102400229459264053d5 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], diff --git a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb similarity index 69% rename from easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 28ef2c7ef618fabc019df802f07457730ee98cd9..3c539b01d11ab2539b815f19f0ba8f1c010138cb 100644 --- a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -4,18 +4,19 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' 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/'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +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'] 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 new file mode 100644 index 0000000000000000000000000000000000000000..f51861712892f3d3088ed5591cc077bfe7cd43e0 --- /dev/null +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'SAGE' +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 = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['da3b135389df1ab9a21288cb041ac0c3'] + +sanity_check_paths = { + 'files': ["bin/freq", "bin/ageon", "bin/segreg"], + 'dirs': ["data_files", "documentaion"] +} + +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 0000000000000000000000000000000000000000..75a920a136dc445a4c4f736fa33f94392f32a85b --- /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' 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 068f81d41af5ae9c447fb52545faf43087db8178..ad73efb9d97c3caff60f68af3249977d1baaee47 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-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..340f9547b81cb4696761761939a6da123c765cb4 --- /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' 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 0000000000000000000000000000000000000000..f62000066175bc24469bed539dd3c70416a34925 --- /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' 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 0000000000000000000000000000000000000000..3167310f24bc4b1343a34b37de34ce04e967f2ee --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-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': 'intel', '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' 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 0000000000000000000000000000000000000000..86a737bc611285559bf5c333a288d58f3a6b0146 --- /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' 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 f7e1fa75aff599483d6a6df25b3dd97c210cd6a2..fb8bdd5fe8813531a28c8e6b9189ecef7d965c85 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 63e54d60a973660207cb3f443487f48ef395d68e..a840cb128c2bfc3d900a164213f317ba0cb4ddd0 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 adc2bceafcb29d6ef68910eb32b974ca1bb0615e..36e2a02cae42ab1ace3fe44e63c5b300405632b4 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 8e693c1ca4205338d31dff48fde7cac059544e7e..b9f3cfb699ab39012e4ea2b0b02543683e0d2346 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 b0d4836a137db8cb488b8f8a4133e1a39c2e3c31..60cfca1ccb14c15eb1e99449652df67b7833d16e 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 b9f29b45c505b7eaa4f1fda31b6f0b4fcfa292d9..1a0f9346211388a7f48e05512492c7829a11ee2a 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 89020e5a6b964fa4d1849be7d3b2b225134a1c2b..4e6810fc240ab9455b24aa0476e1ec4efae60abe 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 f4c56ce013f3c9e5d8e4f9e64b2d63f1fcfdc907..68499c20c9ed4d8a0d8549ff0590861a53300b20 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 f5bdd9828b42f190729fe1fb0bdf05f2b1156633..8e49ec97388d7b77867cd4983eff90836c75993c 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 3f65d37408d342312805a3efce1be9c93bbaf502..6646f63b1d1a50affca4e30690928868ffb3c0df 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 431d04e9dfb3bd4d55d8441f4ffcaf5779ec8e28..6627e15ad70f61dc0e54e3acf428a2d1458e72cd 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 9fb7233435ac8a04fcfe74efffabd6129bbc8f47..e19c44686d5a310925cecad3e76db0433c35ce31 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 b61aa3728e02c36256befbbdc56933e81b65782b..4bbf975f938a84fc07d399a834f9e579b91dca61 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 a98a4841f7a1e834b9b4dbbbe38acba54a5e7624..173ec5abc67b29fdf528f9d5d1172021f1d5cf40 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 ba1a0a43d1dd50f8beca796eae3859f0ac13f27a..a9f67fc8828f42d4b613d78ec8c742f672774414 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 34df491afde567145705a81dc709f9904116220b..5f4f35c9c00028a0884cd3591c3ee12580d357a8 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 a90bb75fa5ab8b3ced38be0d8b099fb943f09f3b..30e51cb632d1495d6dcd6881385c514628e3614f 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' 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 20bc255b1a92698416894bcafc8849611455feb1..5df84b7224749287158c44fcc2232e0aef31b2e0 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' 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 0000000000000000000000000000000000000000..56f2a3c3626e0d82e833a7187276571cbea009c1 --- /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' 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 0000000000000000000000000000000000000000..40cbf3c5592ed3faf4f89916d787d6e2b08f40f6 --- /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' 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 0000000000000000000000000000000000000000..6df761e722d9057d5a268c15c542670f07325b69 --- /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' 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 756efd9115ca042ae4c7f5d226444872eb54a26e..4078e01a54f8283ad512868ed631041f70c910a1 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/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 0000000000000000000000000000000000000000..7e537ec0fb74d1ce0643e97c730dce9f2b7a0ecd --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -0,0 +1,45 @@ +## +# 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 +## + +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' + 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 0000000000000000000000000000000000000000..46e980be5fabb23679bfa8fe332bc4620e30e770 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -0,0 +1,39 @@ +## +# 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 +## + +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' + 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 0000000000000000000000000000000000000000..be020214d208cc75a91f6d54dfb1130f95bc3b00 --- /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' 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 0000000000000000000000000000000000000000..9f5fa19c2405b19b80789b58f2f17d3b5c8e14ec --- /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' 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 3c14ae7d6c46e16d07964cfec85b7865c956cf4c..e137f85d4d652376837dc0afcba2c7b6ce17d430 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 1b4c48aa91e59cd31f3d4bad1803ebc601b6e591..e3ec9ea769af8b16f0707589daa0190b695bdf64 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 0f01678e280d373ac118eff9d1f16d5713941dd7..fd3e7c3888023e778b568833275027a5425d4db9 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 775feb38377e8472ef188e57d8368aa5a883357b..351ac62d2cb0bc6c1f14943a37c82437ea123ff5 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/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 0000000000000000000000000000000000000000..6e5c9aeb32976d72204dbe1dab1279f1e50f3fcb --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -0,0 +1,44 @@ +# 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')] + +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' 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 762b8d99957af08f59524c8893af9cdb094c88c5..4a20471e6de7775fc7f21ac682c733fbe7470599 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 3d66a9ad8c812da537f1c5009c5ae549007bf7b3..9464d9961665bf067e3a79a00fe98ce9d66bc1e3 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 0b67d316a26f1d0c93dc77e38e244c07a873b080..380060ff3b6dd37e4ce9638203595c945cd0f013 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 59be5269fa9a9619efc6548bf2a963fbc932f25b..59c5938c90b232b859f302458c0015bf4c6c694e 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 4df722877b6bedba06d1c157b1456edd7eb8ea6d..36cdd512d2997c56818b682c1826fcdfe8ab052b 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 ba3405a6f52d1826624cd4de9a490cc09663f1d5..44b9de5758aae0b5984b8cac57fbf95b7a337935 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 435de49323320346b15272eb5f61d5d0105fb298..def70b5b622cf9907dac262f86b4c1cf998f9967 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-3.13.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..f7ba78e65490810e94a492d60a75b72717958ad8 --- /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/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 d38cf611011d8eaaaed9f20aee025c8ad36f397e..cb84023340bea0a91d547e3c76dc278c12f7e729 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-3.17.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..41b5a58bd2f43ce24149f8da9f6eec7decf247ff --- /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' 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 62c6f7b8b27a83e63fc4c73b558fc63b36c5de9b..15a228e4cfc9b4bd122434011507cd6bccbfb101 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 06b2583e36b4f279c498c9564c935d861d7b5af7..0e3d5b09430ed07edfbb7cd4c0034e7938a090d0 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 5708afcd84c1c9eda0c27516d457c83ef1e45939..3cdb5e9a31fbfc508208b3558c63f8198434aaba 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 11fc55a1b6d510f66f78708c9c73e8850fad82c8..c9bee3d1d5acad8ec0e9aa6e33a6bf7392a175bd 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 6a41f5863cdd704e90ae0196cf0c304428dfd172..2b1f98a6ac983759dc616a9651729b2bec0cfa3f 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 e06537d494213332b5c58d0eb050d09e907573e3..86716967ffc8b7a52a5ec1b8d1b2ba6da070694f 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 17d369e53012d76db9298c6702f9b97044c1bfc1..70270519d3f01f4ec89fd66243ebb0cba989b8d8 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 26439e2d65f89ff9cec5933ec668459b32f1d701..5c38e72b1ad0b072caa888d6175a1ba6ec6e6ace 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 5d1c89464a85b0bc991c5951a630715a26d2c566..0a07713fbb5ea66d2b195b31db03f56727b7f1d2 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 429cfc37d81766ab26d3097b26b8591d0f7c5baf..408f74829a1280fc3d4b1c81696ff9fca3f6ff63 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 51941069b6bf227a4229e958a20022bc753645f1..5c92bc81368cac969b77db8d56ab73c49839b35d 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 47bee4f6240889b5a75b45f31a7488fb08df1232..8902612f46b4678821d4f7fff6b3065d133b379f 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 8d257ce664be42a42d0878be23fc6ac1846b551b..4b9cea2422164d46c7714aff891e2cf985aa3383 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 c1e564bfd6fbcfc7fedcf2a4e67189d4dabba6ea..d75861cbb66d1b2fcbbf164916054ae7d4139656 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 79c1231084cf1cbade52b54a95b74f2b7e5d060e..177a74a0fbe28fa5296a165de5525f0bbb0f06fd 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 3555a7ac4c102670c5f006fe4693418ae1790fbc..885ab346a94862dd491f56d518f791e813d6bd2d 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 a35ea6d2811fc95f83728004d08f164fc58865d5..46583c5246dd0a8fb355ec1c1c3ad901f34b80e3 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 4eb223b17f20c195ec640ef4c8ce7c0a35924c15..c1a72bbbe4eb833694c78ec0a8e7f9875cca25a1 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 e099c4dd67528427a7fb11f85d0f374ee564aeec..68f9f01974dcd3ff9525ea58d688385095167b98 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/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 0000000000000000000000000000000000000000..9d51ecf299c8c3963cf999f8b6be8f70a60f8e22 --- /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' 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 58fcb58c2d997271b71012d66deeb987ae390a7e..c87beb9409d680024e5903ce83cec0e901e26b69 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 b6190397eea6bf5b7880f26c4bedf94cdb946783..04188b3f1aa186c655082bea1a5ec7f16cbad567 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' @@ -28,8 +27,11 @@ 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"], '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 ee25be84ddca0db5b9433828c1cbeee371758387..457ab933f77dedbea0c46b51107ee9bc2249b048 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' @@ -28,8 +27,11 @@ 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"], '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 406fea6072d167a4b579921a4a55603470206d59..b4f28e006edb94bfd49ee28b19993dd7bcb5aba2 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' @@ -30,8 +29,11 @@ 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"], '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 b04986c691be32dcc52861913199b4b5d6f82984..acf5436cbec2dd0ef0db0d4f1c0f188eadc305ce 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' @@ -28,8 +27,11 @@ 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"], '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 769bc0a35c7132d8fb88b49f83bd890e4f13e743..43cc47b2aa1c809271a9515625463e6fb7575734 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 +31,10 @@ 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 = { '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 fd35161f4863f330cc22f7f7a019b5bda6b73b4d..d8c6f0be04287f0e426a8200720ae397a6efa9a6 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 +28,10 @@ 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 = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], 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 0000000000000000000000000000000000000000..05c3e56c2fab7ebccfd8993a66165b198d31369b --- /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' 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 15d674493593396e9eade81b57bdac12757acf40..bbf5a698d98225fd59beac1ab51f87c568c89c38 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 @@ -1,23 +1,23 @@ # 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'} 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 &&' +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 6ad5e46d49ceaf0caa6a5983a4906de00ca2cc96..352f9013ea58102bda4c8c3ded4086abf7dce5bf 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 @@ -7,17 +7,17 @@ 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'} 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/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 0000000000000000000000000000000000000000..21d1aa5067a0c6508fb733e1c5118084c981af6b --- /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' 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 59a30a98ae95fcb59ea4bff4374e6233b4e284ae..c01885134c992af2a1d53d2617cce3c7a3b37cdd 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 @@ -15,12 +15,14 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb index dddde53b094d892927dddeff3783b4751d2d0571..b19bb39b27115c3a776dcf223856b67f2c794321 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb @@ -15,12 +15,14 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'omp' +buildopts = 'omp FLAGS_OPT="$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': [], 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 c188883666419f7dd6883af2f6afed30adec3211..1ff3f68105a5af4258f2452e79161d5315475915 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 @@ -14,12 +14,14 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'ser' +buildopts = 'ser FLAGS_OPT="$FFLAGS"' parallel = 1 files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + sanity_check_paths = { 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..82347e40147e50d168fed0f7ca9456db9fbad685 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$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 0000000000000000000000000000000000000000..6b97716f509db3aca9e5b874eda6b053319da6b1 --- /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="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..58632f03e4cb8534fe31f7fb60322f825b7c545a --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '4.01' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$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/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 0000000000000000000000000000000000000000..645b7718379ea077aa1894e51676742870312bf5 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-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': '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' 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 0000000000000000000000000000000000000000..d9862520361c27dc4418f723ad118475d0233295 --- /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' 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 0000000000000000000000000000000000000000..b90543199e90bd23033d3f70d153eb0b6da9658d --- /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' 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 0000000000000000000000000000000000000000..c6c18b59b896719376e0af071a9a4e3dea8b3fe0 --- /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'] + +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + +sanity_check_paths = { + 'files': ['sambamba_v%(version)s', 'sambamba'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' 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 d38576ab53b5e95fe1675fd7a8041ea68a4b2e2f..2de8d75b118e363d44bbca158489c38466711fd3 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 @@ -9,8 +9,8 @@ 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'] +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/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..3d67fae22fd89388bb02958341bff692aa8249c9 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.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-3.7.0' + +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/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 0000000000000000000000000000000000000000..c0dc9e45f89a6db0b390e96474539abf5cdd531f --- /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' 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 29459a5481779e8345c16293fde658dcbdcb3204..86ba1ed78fcfcb9a1cab449a63b421728273f586 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 987ce669c8446b7fca760ad28a2504ca37664ebc..2852bb52f53beea1feac3ea9ed2141d1a98501f2 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')] 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 0000000000000000000000000000000000000000..0d3233c81747a060ed01f1bc257c4e92c2c38b18 --- /dev/null +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -0,0 +1,37 @@ +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') +] + +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' 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 f15b6559acfcb79fd47bd0c55b0a5a2981cea879..6af29bdb8bf4ff672d2230b46fd790c108d12ec4 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/Spack/Spack-0.10.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..3a97b911b1c3495c60981797752c6884ebea98ae --- /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' diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index fae61083b0ea89060a719ec6368d46977f3260d5..41b36d91f6b7471e5b76a8421fa2407b97688a32 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')] 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 e8b9b26666b35fc1eeb190dfb46f1b3d93e09ef5..656bb0f55e89598c84d639991c0922353585c92e 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 a58b6b19e0b507ef2072cc8abc64fdd5fc52034a..26cda8da07a3deeb96127e1e83c9b8c8e0a3aab8 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/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 0000000000000000000000000000000000000000..9ffb95010075b2b5cd740feb8516ef098fb6c486 --- /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' 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 0000000000000000000000000000000000000000..4b5fa1bf48b94415dd0ec032c343c1e9872cd740 --- /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' 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 0000000000000000000000000000000000000000..122fdfc60dcc455ea30093b5d0a2fb5088a67c1b --- /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 $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/' + +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/Stacks/Stacks-1.03-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb index a99ef374cd70174a61af46c94247b45440477ad8..5590d0a6b095b2c8a472dde43d0b996d6893ebd3 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 a9bfd6bbb414a96641864cb9c96e16fdebe25af7..005b7b2b5728a35f84fc6d4976766cb4c2a26eb0 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 189d7f6db0caae13bbc990311e8eff217fe923f6..197e799318ae826633c6354725790ba8b67ca015 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 6d5d6358c842bdfc156a56a5761834999be5bf02..e042becab7ed989272fb91a5c85b43ac2c529a43 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 new file mode 100644 index 0000000000000000000000000000000000000000..1df7d789c0aea115f59d5d31eb1edc9187287cd2 --- /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' 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 0000000000000000000000000000000000000000..4f24751d68768efec19062ded0317f0f1a5910d4 --- /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' 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 0000000000000000000000000000000000000000..341b4db710aea32ffb799717d365367da08cf4d1 --- /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/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 0000000000000000000000000000000000000000..1c6a84db5e4b44b00771e334442266e2910fc0ad --- /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 0000000000000000000000000000000000000000..ce59a23011805d67a1ee33aa369d7977186b3620 --- /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 + 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 70ca06ed7656fef1ac059c6bb80d75d95ab0d2aa..f2c6a5db74d25128e912fa05ba105c13473c0132 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 424d2b7aebc3f281cdd096d43352700945858870..69634c30e6ad8b812118421f021606c127fbdf0e 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 new file mode 100644 index 0000000000000000000000000000000000000000..2476496f2d911a030954c704d4736da1eb04ae42 --- /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' 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 be6f1332e2d701f6a307a316f2fcf43badc45774..cf172a3cf0c96d9d9e80658ef11a33164137aa17 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'), 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 0000000000000000000000000000000000000000..3f7ce4f28fdcd4b416c3f4546edbf4d25e263e49 --- /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 0000000000000000000000000000000000000000..28aa92c03a69ea86df563e491718470156c4093d --- /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' 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 de900f73b252c87ce2f6cfc2d5885146de032751..01689413cc54da79735a9df968469bc707e986e7 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 58f5db7a334f89214d49c51ef553a445326582b4..2c00792f81569f5dfe8a499619c9d5139e93900f 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/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 0000000000000000000000000000000000000000..c2c5a38e56ae865c5eff1623cfd058a60a2fd304 --- /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' 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 0000000000000000000000000000000000000000..7a02acddeed3ae25fa0a6751735ef7e2287aa84d --- /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' 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 512dbbe733f7f257e0767a8adad7c4554a0c594f..6f12c299b1e526f1c078cc3b9f24ca286b7c4b99 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/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 0000000000000000000000000000000000000000..a99c1c09125d6262ca110a974a815b1ba5ab1cfc --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-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 = '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' 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 0000000000000000000000000000000000000000..9e8395819b813dd186a3f0e1f2befa1b509df177 --- /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 0000000000000000000000000000000000000000..dd9bbeb576e2cbf7b59299a2bbbb9b5cb7da2e90 --- /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 0000000000000000000000000000000000000000..ad5177d70b7507161dfff79014d8d40df510b9f0 --- /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 0000000000000000000000000000000000000000..8d85cb18f49f3c7cbba528bdc6b15427e1b54635 --- /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' 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 a6ab83c9a798f8f2b22848575281a2fc1fb043e9..1d1ef64120626441a97a0101999928cc56d70533 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/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 0000000000000000000000000000000000000000..523cf018d914a39148de58e638f18755c3c12dd0 --- /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' 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 0000000000000000000000000000000000000000..1372c5db1ed18e9cbfdc22f21060dc64496fa9f7 --- /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' 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 39c950b357de89b301a95036ce25a19d4ae03cbf..a9245a0b765630c5682a1b4540d3fb69fb4171ce 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/sickle/sickle-1.33-foss-2017a.eb b/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..aad6c785a517d417f8f1e6b8440e0d2ebf2f7078 --- /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' 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 0000000000000000000000000000000000000000..6caab74f6e0c00e18083c2b78d633ffa5c0bc404 --- /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' 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 0000000000000000000000000000000000000000..c70dfa11d6cb4ae2e50b9ecebe7c952359b340f2 --- /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' 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 0000000000000000000000000000000000000000..c65762eb7a179daa4ce566855ce4ec5ac24c8f75 --- /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 $LDFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3261c207aaf36870adebb29252f380a0ec4a9737 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' 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 0000000000000000000000000000000000000000..32f208ded504b40773330cf205b5ba54d67692d0 --- /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' 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 0000000000000000000000000000000000000000..6c2b70d3f7ec4c75724f272b6d351df777e622ef --- /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/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb index e2411ef3f5963afd41e6a3696fb7c836d5ecacf2..585ebb993230e094e50238e611eca8acef958295 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('.', '') 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 0000000000000000000000000000000000000000..435f33a3bd0cb81d02f95e92268395a8c673edf2 --- /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' 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 241a1d5fbffd4c00660499cb945886844c5d629f..7c1426364fb970f6f548bfc82df3da28805778a7 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/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 0000000000000000000000000000000000000000..e91ebd2437620657b9837671eda231bf43f0461d --- /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' 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 6ab91f87e3caafadb1f5d77115bae5cbff8cdf1c..1ee4a4a0bc64a347598cc36359f3ec50506f7eac 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 09140f6d09e00224c5e33da0f635477dd2b84052..1c13652bc7d2dfc68655111a2c47e10d92aa8386 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 2f2888a832174aa297859e7d9d12b4723cdbf17d..72a246892c2acc7d5f6654c928441ff54d7342eb 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/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 0000000000000000000000000000000000000000..3d473ebedb212373663ebfb365e2f8ae28432230 --- /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/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 0000000000000000000000000000000000000000..9dca9f6e5cc5e72ccd5373e344ae31bd987a55ca --- /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' 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 0000000000000000000000000000000000000000..b94ca618c9b8f2aa9bb1ad005adc55ae135d1ad8 --- /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 0000000000000000000000000000000000000000..d8b29474228f408421e81d904836b0c2db25ce40 --- /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' 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 0000000000000000000000000000000000000000..8ccd735bee54751a955b581e11869adfacc41c57 --- /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' 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 0000000000000000000000000000000000000000..4898d79427ad87e87974a7aae531a42948ffbc72 --- /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' 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 0000000000000000000000000000000000000000..f1c3f15e89395b55da9b672a76f3222297f8a2c5 --- /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 0000000000000000000000000000000000000000..42b703619c8541ff9636f2d13f595d6aeacf9ae4 --- /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)sm-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' 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 0000000000000000000000000000000000000000..0c78137460b7982d85546893d46587df934bae2e --- /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$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a01bad3db98f6a431293e4fa608d4b9f10ac5667 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('X11', '20170314'), + ('Tcl', version), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' 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 0000000000000000000000000000000000000000..77785bc785105f837c26df366c726f9be1dd1214 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.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': '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'] + +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' 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 0000000000000000000000000000000000000000..166329f4f1734b1cf5a49ca385bbb33d81caa969 --- /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' 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 a89bd3216ae95b6189d1f43939cda6d2bb4be060..091f914cb3b0491a2352f53bf000318eb65d9478 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/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 0000000000000000000000000000000000000000..4ddd5946b84f52834433de641cbc7ebf15a3e1b6 --- /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\n""" + +sanity_check_paths = { + 'files': ["trimmomatic-%(version)s.jar"], + 'dirs': [""], +} + +moduleclass = 'bio' 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 5f116c4b08e19272176c1f95631dabc8bfeb8f56..71643e32bd64158355b7b93feb5ffd8f549eac7b 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 58018d93350fd5ff63bec5cba9c884c7d02fb328..181142b3dbf262d701260a5ea6083c1357ff3922 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/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb new file mode 100644 index 0000000000000000000000000000000000000000..c81d846fcaaf18586fd01c2976eb3daaea17771e --- /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' 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 0000000000000000000000000000000000000000..f90202e1b4333c7d0984b81be4c12c79322a8934 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +moduleclass = 'lib' 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 0000000000000000000000000000000000000000..fc7398b13b223ccd2c0031cbda60040eefb90a90 --- /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' 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 0000000000000000000000000000000000000000..1413bb1d34fff1c40ada9d43dc2df254cf9c4c23 --- /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/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 0000000000000000000000000000000000000000..0c3651f6d7c7cc3139b9b39fcf471afe9a6e8fc5 --- /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/t/texinfo/texinfo-4.13a.eb b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb index 1f3105220a9c5a73edd2dc9e5a13aa68b188a8b7..02d5fea5deccccce747a6fb105315deabbe0b579 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 e8a270b38c02749e6baf9a09f86291dd844ea7b7..c524f8585763e605bcec87898bf0d78259a0c9b5 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 0eff73d3ccb746a330deb7df1086f2ade67b4430..a4b5f9fb2623c0c9c0924919a93f3042b28d0e93 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/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index 8b0f6b51a85ab79229a735fd626bd347401af5b4..6125b3dd3885740ed5565cf833bd237d31d6eb3e 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/%(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 391b43238fd170e9c1b173c66ec2491500faf1d1..bb013b1619c3c32797903f7fb77372f39abb8e41 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 new file mode 100644 index 0000000000000000000000000000000000000000..f419b0b85cd9b8af84b374504030f7953b6db514 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +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/%(name)s/%(name)s/releases/download/%(version)s/'] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' 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 0000000000000000000000000000000000000000..0423702965f5afbda60173c884610a119d044612 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -0,0 +1,27 @@ +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': ''} +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' 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 0000000000000000000000000000000000000000..0e89a4b4d60a782be26374d46d1b22f1e14ca3ad --- /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' 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 52e94958738237964c1195c827a6471e9ddc876f..cc2a64b9ff347dca6193ab3aadb2318629e6725d 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 961153d9b47f8f658584e76fa77486b4f3d865f3..d2a22ed8a6ade41408cca3f80103bfe76683b4aa 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 07e180dab52d731d0fcd579764c90d78627106fb..c09d3e96a204e13194a434066a28b5434ff591d8 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/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 ae04827ae1a568d80bb05ec99f00afd6ee8b7ca2..ce865ad5b9c9aec58d9c50f48651676b003b7c69 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/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 0000000000000000000000000000000000000000..3495ebee0c0a5ea6c6ed2e26e7df24d80d6b79a4 --- /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' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..3e3df4bec479b2902698dd3cfa2824bc9ea73279 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.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 = ['vmd-%(version)s.src.tar.gz'] + +patches = ['VMD-%(version)s_configure.patch'] + +checksums = ['5706f88b9b77cc5fafda6fef3a82d6fa'] + +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 0000000000000000000000000000000000000000..23f1311b5b061610ca1ad00e2947679739d550ba --- /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 diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..71edba0d68c65d32a7caef759763e63325972371 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,60 @@ +## +# 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 = '6.3.0' +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'), + ('X11', '20160819'), +] + +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', 'ParseOGLExt']], + '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/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 0000000000000000000000000000000000000000..ff2f4a0f6303c8defae0ca6b7d542fd5a6b39ecf --- /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' 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 0000000000000000000000000000000000000000..5db4d180babb68b45724d01e9e03f7c31af8f5a8 --- /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' 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 ba30d5877f8ee1fc53f08eeaf857fc51cd80eff8..af1032ae7a8d4bf0bc1f4a8add4ceb9bd08f49a3 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 $EBROOTVARSCAN/VarScan.v%(version)s.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 186dfc58cc4ee8aa08a1990858849f0fb7089059..dd6c6f31b089ff85efceca088f50bb40ba50f8e5 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -23,8 +23,6 @@ sanity_check_paths = { 'dirs': [], } -modloadmsg = """ -to execute: java -jar \\$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/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 759ecb7840e83e1ba0c439c5bb2ec7a88c6bd477..45a8cbb1a5a7eeb4669f20267b005efe47384d41 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/%(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 f0b402025371329db9087c9c188aa613cd950eb7..fafae9335ef7443b3424010fa2008a1d2833f935 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/%(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 106d2f71e31e8705848bfcfcf29914429fc8a6fb..29c51c10302ddb52177445faf35ed8bb942d203d 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/%(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 new file mode 100644 index 0000000000000000000000000000000000000000..3214395e25accd0eb0473d3996afec3fb2da498f --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -0,0 +1,46 @@ +## +# 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/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': '2016b'} +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/'] + +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"' + +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 0000000000000000000000000000000000000000..b53cab1ffff52a057b1d5aa74e28e052f979c286 --- /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); 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 0000000000000000000000000000000000000000..ec625ff6c6a87d90354e8367522cfbf724942c83 --- /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/%(version_major)s_%(version_minor)s_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' 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 0000000000000000000000000000000000000000..fc2a6f62b89fb2ba00683733a7b0cb6f95667095 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -0,0 +1,46 @@ +## +# 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/'] + +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 +# 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' 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 0000000000000000000000000000000000000000..674a6d44d51ffb924fd363bb8ea99bfee2a1236c --- /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' +versionsuffix = '-Python-%(pyver)s' + +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') +] + +configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimdiff'], + 'dirs': [], +} + +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 0000000000000000000000000000000000000000..c38a164cb963a77b71cf09983bd5742ce706eab4 --- /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 0000000000000000000000000000000000000000..c821c18048eecd24f6b590f16e3969bf6e4e9c56 --- /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 0000000000000000000000000000000000000000..b31dee5a6e310c12c9f11efcb3ec2cfc553c6bad --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -0,0 +1,34 @@ +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')] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +# 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]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} + +sanity_check_commands = ["mympirun --help"] + +moduleclass = 'tools' 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 a65ca2295bb5b413363782b9ab37c797e52b69c2..c6a5e3fa1409d49e8ea46e9fb428f562f878d3fd 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 @@ -31,10 +31,8 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} -modloadmsg = " execute WEKA: java -jar \\$EBROOTWEKA/weka.jar " +modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 396230d2a7d10f1aabd6af04d686cdf70f835760..96ac9d6530ba3e488c4684abc3cd5e77b0559446 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -31,10 +31,8 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} -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/WPS/WPS-3.8.0-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.8.0-intel-2016a-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..ed55b813b21afd02cc5a142eedcc06ae2bf82b4b --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8.0-intel-2016a-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WPS' +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 + 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_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +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_known_problems.patch', +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('JasPer', '1.900.1'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.8.0_known_problems.patch b/easybuild/easyconfigs/w/WPS/WPS-3.8.0_known_problems.patch new file mode 100644 index 0000000000000000000000000000000000000000..e94fa09a3a2d838f6e3394870ae82c991ed3d0da --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.8.0_known_problems.patch @@ -0,0 +1,39 @@ +# ====================================================================== +# 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 2016-06-30 17:18:27.000000000 +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 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 0000000000000000000000000000000000000000..a0a5dd6390283a1d4f932d233f4fde07351029ea --- /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-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 0000000000000000000000000000000000000000..55b59e16083c6dc9adf3a11c8c08479a45e78473 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -0,0 +1,25 @@ +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'), +] + +# limit max. parallelism for build (WRF-Fire will cap to 2 if > 20) +maxparallel = 10 + +moduleclass = 'geo' 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 8afc4ff82211220f78934d2a3cfc6a362833d419..e63ecee8b4ce4156ac4eebaf02910bbee6082d22 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-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..09959e26a3f8bd71050622b9f628105ebcdc5c04 --- /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'), + ('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' 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 0000000000000000000000000000000000000000..4e591faa377367cfeff95cfb0874a9992621e55b --- /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 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 0000000000000000000000000000000000000000..494521239325f61275c0e021d41f1b64ef440bc8 --- /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' 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 0000000000000000000000000000000000000000..277bc0108a836cc94b17d11cae3e7e8ae289d694 --- /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/x/X11/X11-20160819-foss-2015a.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..94c5bfdb697d20688db3e2474df029398b600a70 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb @@ -0,0 +1,133 @@ +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'), + ('Bison', '3.0.4'), + ('gettext', '0.19.4'), + ('pkg-config', '0.29.1'), +] +dependencies = [ + ('freetype', '2.6.2'), + ('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' diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb index c44e65c206b3e505bc4a5ff5630443c0a5d0c474..fbaa5cf2db697d6a3ef2fb1f561aafd51fb59afb 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 556bda9f6eb6ed8d8e21799201a95af3ac63ddd5..586cdcf5d6226f3c6f244c145f5eb4c81d284e88 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 = [ 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 0000000000000000000000000000000000000000..2e89d51b91f39b82b22db1649e604ad086318a32 --- /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/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 0000000000000000000000000000000000000000..dc3461eb7f4fc654b104101fface3582c3019dbe --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -0,0 +1,136 @@ +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', '-libpng-1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('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' 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 0000000000000000000000000000000000000000..0423282a10869512a423d2ae1c690efc04e3cbc4 --- /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' 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 96695c9d5cb9eb2bba5805f6c4cc13cf76982823..6c49a4458b97f7799e0d6e9f15d42c0c4e670f94 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 f08ddf7da4a28196e65d2c12dd3256ed5cfdf1f2..001a737c6ef0dd27b52345bab94f6eaee308a145 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 d4f3584da4bbfb5ed53d5c39421925bcd707a00a..f5d80fe9e55caa6303de63e3fc109fb1cdf8e9a7 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 90393732b9c2a2c07caef233f465c51fa291bd2c..08aad5d870e7e959f99810a985c382613afaad0b 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 52273a7c6b698923b372b19f8dfa783914c2e10f..deb8d13a10f307542678eb91a65cfeb7ce1d95c4 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 8985ebbf18886d1967f9684951a071428b8ca5bc..a0c7f313e03200e06aa3c858451b7d7e18945021 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 aaea1f659f17154fa8f0bfee51ccef7a12f39ef9..e891d5536ae59cc17c5172298e0dddad0791f73b 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 1b63e653414033c230bdf4ef69399761b79d2ebc..4c118e934ff4e5fbe947be25febb0f96e425e192 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 2cb7040caf5d6caae85f8256aedd5873ebe71f17..43117900f609de6d244efb844a21df60614ee679 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 98229490710a6428e519ddb066ef776cbb774986..0e6f109230e0783ec95dfd92e113a5e04c5529d4 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 bcd46743d29b779fdf30a48946c41f6ed2e36530..fdf1453ac4a8b10dc555b242d5e9d05a7e65edee 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 95304a848da78fc16f1e2f1650b59ac862fa9f17..85431b3d6e9e08e2146ba71adbbdfcf38baee95d 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 0000000000000000000000000000000000000000..3090e4e0eacb0770adcf793487b42ad7c976b101 --- /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; 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 0000000000000000000000000000000000000000..735c3cbe5ba90ee0d34aee634ca051df83f6e74b --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +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/'] + +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 + ('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' 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 0000000000000000000000000000000000000000..6b2b631d5139587070d4108948b7644d8c438032 --- /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' 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 0000000000000000000000000000000000000000..b44af67ba6d5c8ebbf2ec00e6b13c80eb6856126 --- /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/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 933c8b66d87f6dda094f191b46cceab045807c93..3b7e3d4f5dfe35c6d0dda4d1a8e3473328d43a27 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/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 0000000000000000000000000000000000000000..2e98d1a81ebf784a267ed18378152ff79337dee9 --- /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 0000000000000000000000000000000000000000..52e3d066e8286a7ca91760975f6fd919a6320901 --- /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' 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 0000000000000000000000000000000000000000..6f48acb1542972cfe8bfac661ec9a48e1ed85ae8 --- /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 0000000000000000000000000000000000000000..06e2a620f7b0e0ecc35817def423c103370853c8 --- /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' 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 a6e0dada54a528d3e8af62dff6eb94e2e940af95..eeebc684bc7491955b5d899d4989e0c1efd7cefe 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 4d7005749aa29b183c07b8f413d55cb0da6d86cd..4610fe64fde19eb3e81b6092573d062150e79128 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 new file mode 100644 index 0000000000000000000000000000000000000000..bfb9412cfce42a4615e58e4f3eb5617b6c008cfb --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,65 @@ +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', '1.5.2', 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'), + ('bzip2', '1.0.6'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('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')], +} + +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 1c86ea984c5350f7ca61a8ccf6acbe329e57509c..5623f2e81c05f485ecf16381269f6182f990b89f 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' 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 0000000000000000000000000000000000000000..e82ea4a1aeda1a91c998721a8fbd3c75671d5298 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,64 @@ +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'), + ('bzip2', '1.0.6'), +] + +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')], +} + +sanity_check_commands = ["python -c 'import yade'"] + +moduleclass = 'devel' 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 0000000000000000000000000000000000000000..d40e39150a0219621316f2454ebcddcfba8b1947 --- /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' 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 0000000000000000000000000000000000000000..bae739cbfae6f163accd6595e0cda71e29820e2e --- /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 0000000000000000000000000000000000000000..f0db7e825680b7e642a01f21bef5049c01e5abc8 --- /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' 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 0000000000000000000000000000000000000000..9f5b1ed999a4fd67195c6d81ca3279d5c591ffdb --- /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' 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 2e2077d5990de7ab2045762249a73e6e59ce53c0..f85c7f00dd890caf4648c1e2e934f6b9a46ac4b3 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 b5d9aa81e3f91d3d5fd7524252f2599247ba8e28..4c59674a12f9439ab6cf05aea4277c870572ce04 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 ' 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 0000000000000000000000000000000000000000..165ba15944d71df5f55406391615532efe433a84 --- /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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb index 02bb809a0bc1dee6f8d8327b4378bd2fca1458b2..df836d072b78a9f6c8c3b92cfb4a88368a676564 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 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 0000000000000000000000000000000000000000..8409e2aa5cb8ed8aa6211baecdf765d48b085e2c --- /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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a15fb20fe6433ddec02228a31db390c489f17cbc --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.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': '6.3.0'} +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', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' 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 0000000000000000000000000000000000000000..bec9454ed8e02837b2cb71059ecdc880dc6eef3a --- /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' 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 0000000000000000000000000000000000000000..b74939ef095a74fd162359b48a31781ac0c1aa81 --- /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' 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 9daa7bba8182133977431cf5fd1853b3a90eac0d..ab2a54c1b69090e866ecc3ec890ef34b805b05f0 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 ec75812a654e6ec398b01dbd423827200f643310..8b079f0d60df1ad6e69f3fe29e40d65ef9a66d2a 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 20e9ee0821fecae65ebde227727300591748be3d..8986e89a6dfb39f0cfb52f60f232e2c14dc6d37a 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')] 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 0000000000000000000000000000000000000000..5c5b309e9038dc1bbd1dc285e380532135a5d23b --- /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' diff --git a/setup.py b/setup.py index 3979a91f642d0618632b821bd48ed2d69f660a81..85590c2983f602d80262249a49b60c9bd62df8a4 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), @@ -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 = '3.3.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 551695c2591a5e250d6a7af1067548de16e10314..993e9395bac8bb49f3d9703457a53b041e335a1e 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)