diff --git a/.travis.yml b/.travis.yml index 1100abe24e94956edf91aec41ef65e190ed1c035..13ca5c06124cde891f9985517b0315b7d63358b2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,16 +2,20 @@ language: python python: 2.6 env: matrix: - - ENV_MOD_VERSION=3.2.10 - - LMOD_VERSION=5.6.3 EASYBUILD_MODULES_TOOL=Lmod - - LMOD_VERSION=6.3.1 EASYBUILD_MODULES_TOOL=Lmod EASYBUILD_MODULE_SYNTAX=Lua + - 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=6.6.3 + - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=7.0 + - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Lua matrix: # mark build as finished as soon as job has failed fast_finish: true include: # also test default configuration with Python 2.7 - python: 2.7 - env: ENV_MOD_VERSION=3.2.10 + env: LMOD_VERSION=5.8 addons: apt: packages: diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8501454d3737f8f1bde8e94ceca8613b3bb379e2..44fdf028c3bf35fd2778d0637faeec16addb3d17 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,132 @@ 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 6,548 easyconfig files, for 998 different software packages, -37 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,225 easyconfig files, for 1,123 different software packages, +25 different (compiler) toolchains, 13 software bundles and 1 meta-package. + +v3.0.1 (November 30th 2016) +--------------------------- + +bugfix release +- added example easyconfig files for 7 new software packages: + - Cookiecutter (#3827), ETE (#3857), findhap (#3860), graphviz (Python bindings, #3826), LoFreq (#3856), + PhyloBayes-MPI (#3859), XGBoost (#3849) +- added additional easyconfigs for various supported software packages +- various enhancements, including: + - add ipywidgets and widgetsnbextension extensions to IPython 5.1.0 easyconfigs (#3818, #3823) + - run dadi test suite as a sanity check command (#3858) +- various bug fixes, including: + - fix incorrect descriptions for ifort (#3817) + - fix modulename for Jinja2 and Pygments (#3823) + - fix download URL in BLAST 2.2.26 easyconfig (#3861) + + +v3.0.0 (November 16th 2016) +--------------------------- + +feature release +- backwards incompatible changes: + - archive easyconfigs using old inactive toolchains + - see #3725, #3728, #3729, #3730, #3731, #3732, #3733, #3735, #3736, #3737, #3738 + - only taken into account by EasyBuild if --consider-archived-easyconfigs is enabled + - no easyconfigs available outside of archive for QLogicMPI + 15 toolchains: + - ClangGCC, cgmpich, cgmpolf, cgmvapich2, cgmvolf, cgompi, cgoolf, gmacml, + goalf, gpsmpi, gpsolf, iiqmpi, intel-para, ipsmpi, iqacml + - fix name in PyTables easyconfigs (was pyTables) (#3785) +- added example easyconfig files for 32 new software packages: + - 3to2 (#3655), Anaconda2 (#3337), Anaconda3 (#3337), ART (#3724), atools (#3631), + awscli (#3645), behave (#3751), Blosc (#3785), bokeh (#3790), Cantera (#3655), + Cargo (#3764), dadi v1.7.0, distributed (#3786), ea-utils (#3634), Elk (#3644), + FGSL (#3638), gencore_variant_detection (#3337), help2man (#3768), lbzip2 (#3791), + Log-Log4perl (#3574), Minimac2 (#3783), mypy (#3694), OBITools (#3573), + perl-app-cpanminus (#3337), PGDSpider (#3625), prokka (#3755), Reads2snp (#3609), + spglib-python (#3620), SUNDIALS (#3654, #3655), SelEstim (#3626), XMLStarlet (#3797), + x265 (#3090) +- added easyconfigs for new 'intelcuda' toolchain (#3750) +- added new easyconfigs for existing toolchains: + - goolfc/2016.08 (#3796), goolfc/2016.10 (#3666, #3775), intel/2017.00 (#3543), intel/2017.01 (#3757), + iomkl/2016.09-GCC-4.9.3-2.25 (#3680), iomkl/2016.09-GCC-5.4.0-2.26 (#3772) +- added additional easyconfigs for various supported software packages, including: + - Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, Octave 4.0.3, + OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 6.0, Rust v1.12.1 +- various other enhancements, including: + - STREAM builds using ~56GiB and ~111GiB (#3670) +- various bug fixes, including: + - fix source spec in VASP easyconfig, ensure static linking with Intel MKL (#3381) + - fix source URL in GCCcore 6.2.0 easyconfig (#3608) + - correct STAMP dependency in i-cisTarget, must be 1.3 (#3613) + - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#3623) + - fix source URLs for Cython (#3636) + - add Bison as build dep and M4 as runtime dep for flex 2.6.0 (#3656) + - enable parallel building of flex 2.6.0 (#3630) + - add zlib and bzip2 dependencies to X11 bundle (#3662) + - use 'letter_dir_for' function rather than just grabbing 1st letter of software name in easyconfigs tests (#3664) + - add patch to fix typo in GRIT 2.0.5 (#3675) + - fix typo in patch for WRF 3.8.0 (#3702) + - use $CC,$CXX rather than $I_MPI_CC,$I_MPI_CXX in patch for OpenFOAM 4.0 (#3703) + - patch FLTK to fix 'undefined symbol' issue when building Octave (#3704) + - include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself (#3723) + - update Travis config w.r.t. changes framework config defaults and required Lmod version (#3773) + - don't limit parallellism to 4 in recent GCC easyconfigs (#3776, #3777, #3778) + - include M4 as dependency in flex 2.5.39 easyconfigs + fix consistency issues (#3782) + - consistently apply patch for ncurses 6.0 (#3792) + - eliminate dependency on mpi-mic-rt in ifort (#3793) + - include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs (#3794) + - make OpenBLAS use the LAPACK version specified in the easyconfig (v0.2.18 & v0.2.19) (#3795) + - include original download URL for ISL source tarball in GCC easyconfigs (#3798) + - disable installing libiberty for binutils built with intel toolchain (#3802) + +v2.9.0 (September 23rd 2016) +---------------------------- + +feature release +- added example easyconfig files for 88 new software packages: + ADMIXTURE (#3359), angsd (#3593), ASHS (#3429), AutoDock (#3465), AutoGrid (#3466), BayeScan (#2748, #3356), + BayPass (#3451), Bazel (#3379), Blender (#3553, #3558), bwakit (#3567), BXH_XCEDE_TOOLS (#3410), CastXML (#3403), + CHASE (#3304), configparser (#3368, #3424), configurable-http-proxy (#3380), cppcheck (#3508), CRPropa (#779), + DicomBrowser (#3432), DMTCP (#3422), entrypoints (#3368, #3424), f90cache (#3570), fastPHASE (#3343), + fastQValidator (#3192), FFindex (#1135), FragGeneScan (#1198), gdc-client (#3399), gflags (#3417), glog (#3417), + GRIT (#3561), H5hut (#3431), HAPGEN2 (#3344), HEALPix (#779), IMOD (#1187, #3347), IronPython (#607), + jhbuild (#3476), jupyterhub (#3380), Keras (#3581), khmer (#1158), LeadIT (#3345, #3599), LevelDB (#3417), + libbitmask (#3481), libcpuset (#3481), LMDB (#3417), log4cplus (#1136), MACH (#3346), Mako (#3460), Maq (#3428), + MetaGeneAnnotator (#3307), Metal (#3324), Mono (#607), MyMediaLite (#607), nco (#2575), nose-parameterized (#3579), + OpenEXR (#3553), OpenImageIO (#3553), path.py (#3368, #3424), PCRE2 (#3325), pftoolsV3 (#3317), PHASE (#3385), + PLAST (#3288), PLINKSEQ (#3402), POV-Ray (#3551), ProbABEL (#3108), prompt-toolkit (#3368, #3424), + protobuf-python (#3563), PSORTb (#3317), py (#3403, #3482), pygccxml (#3403, #3482), pyGIMLi (#3403, #3482), + pyplusplus (#3403, #3482), PyQt5 (#3533), Pyro4 (#3527), pytest (#3403, #3482), QCA (#3595), RDMC (#1137), + S.A.G.E. (#3427), SDL2 (#3551), SHORE (#3531), SimVascular (#3555), SortMeRNA (#3326), SUMACLUST (#3316), + SUMATRA (#3316), Text-CSV (#3323), Triangle (#3403), VEGAS (#3457), VirSorter (#3307), wcwidth (#3368, #3424), + X11 (#3340) +- added new easyconfigs for existing toolchains: + - CrayGNU + CrayIntel 2016.06 (#3377) + - foss 2016.07 (#3517) + 2016.09 (#3523), + - iomkl 2016.07 (#3458) + - pomkl 2016.09 (#3516) +- added additional easyconfigs for various supported software packages, including: + FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0, + OpenMPI 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0, + Yade 2016.06a +- various enhancements, including: + - adjust PSI4 easyconfigs for updated easyblock (#3312) + - clean up libxml2 easyconfigs according to updated libxml2 easyblock (#3479, #3509) + - significantly speed up verifying of dumped easyconfig by resorting to 'shallow' parsing (#3520) + - include sanity checks for all MATIO config files (#3528) + - remove --with-tcl-config/--with-tk-config from R easyconfig, already done in R easyblock (#3580) +- various bug fixes, including: + - disable testing in all ParaView 4.4.0 easyconfigs, required download is too much of a PITA (#3178) + - add SQLite as dep to GDAL 2.1.0 easyconfigs (#3342) + - add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs (#3342) + - add bzip2 as a dependency of freetype (#3464) + - specify correct MPI target in FDS easyconfigs (#3488) + - add tcsh as OS dep in NAMD easyconfigs (#3491) + - statically link ncurses/libreadline in Lua easyconfig with 'dummy' toolchain (#3545) + - add M4 as dep for flex 2.6.x (#3542, #3550) + - add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs (#3548) + - make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix (#3556) + - add missing patches for extensions in Python 3.x easyconfigs (#3557) + - add missing XZ dependency to libxml2 2.9.4 easyconfigs, change gettext dep of XZ to build-only dep (#3568) + - enable running of tests for HPCG (#3578) + - fix buildopts in tabix easyconfigs (#3584) v2.8.2 (July 13th 2016) @@ -996,7 +1120,7 @@ v0.8 (June 29th 2012) --------------------- - added support for building/installing 17 additional software packages: - - BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, Maple, + - BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, Maple, MrBayes, NCL, netCDF, netCDF-Fortran, Szip, WPS, WRF, zlib - the build procedure for WRF and WPS includes running the tests available for these packages - various bug fixes and enhancements: diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..264a6e4ac8233d37303084d292657fe6e6a11470 --- /dev/null +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-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': 'intel', '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/__archive__/README b/easybuild/easyconfigs/__archive__/README new file mode 100644 index 0000000000000000000000000000000000000000..37371576b7fd9e3da42b758b973dbf8b7259c633 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/README @@ -0,0 +1,10 @@ +This directory contains archived easyconfig files. + +Reasons for archiving easyconfigs include: +* old/obsolete software versions +* use of deprecated toolchains + +These easyconfig may or may not work with current version of EasyBuild. They are no longer actively maintained, +and they are no longer included in the regression testing that is done for every new EasyBuild release. + +Use them with care, and consider to use more recent easyconfigs for the respective software packages instead. diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/a/ALADIN/ALADIN-36t1_op2bf1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/a/ALADIN/ALADIN-36t1_op2bf1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/a/ALADIN/ALADIN-36t1_op2bf1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/a/ALADIN/ALADIN-36t1_op2bf1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-no-OFED-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-no-OFED-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-no-OFED-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.10.1-gompi-1.5.12-no-OFED-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb b/easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb similarity index 100% rename from easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb rename to easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb b/easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb similarity index 100% rename from easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb rename to easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb b/easybuild/easyconfigs/__archive__/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb similarity index 100% rename from easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb rename to easybuild/easyconfigs/__archive__/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb diff --git 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b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/__archive__/i/IronPython/IronPython-2.7-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/i/IronPython/IronPython-2.7-ictce-4.1.13.eb new file mode 100644 index 0000000000000000000000000000000000000000..147957947e3842bcd27cb64f58f60c036f3ac925 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/i/IronPython/IronPython-2.7-ictce-4.1.13.eb @@ -0,0 +1,16 @@ +name = 'IronPython' +version = '2.7' + +homepage = 'http://ironpython.net/' +description = """IronPython is an open-source implementation of the Python programming language + which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and +Python libraries, and other .NET languages can use Python code just as easily.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['https://github.com/IronLanguages/main/archive/'] +sources = ['ipy-%(version)s.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-11.1.073-32bit.eb b/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-11.1.073-32bit.eb similarity index 100% rename from easybuild/easyconfigs/i/iccifort/iccifort-11.1.073-32bit.eb rename to easybuild/easyconfigs/__archive__/i/iccifort/iccifort-11.1.073-32bit.eb diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-11.1.073.eb b/easybuild/easyconfigs/__archive__/i/iccifort/iccifort-11.1.073.eb similarity index 100% rename from easybuild/easyconfigs/i/iccifort/iccifort-11.1.073.eb rename to easybuild/easyconfigs/__archive__/i/iccifort/iccifort-11.1.073.eb diff --git 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rename from easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-iccifort-2011.13.367.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-iccifort-2011.13.367.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-iccifort-2011.13.367.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-iccifort-2011.13.367.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb similarity index 83% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb index 104ad6a3bde2127f348767ec3b8b17b37dbb88fa..cda9d848b716bd766ef479b3582168ac7ceef36a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel-para', 'version': '2014.12'} 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 = { diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-4.0.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.1-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-4.0.1-ictce-4.0.6.eb rename to 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a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.2.7-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.2.7-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.2.7-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.2.7-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgoolf-1.1.7-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgoolf-1.1.7-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgoolf-1.1.7-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgoolf-1.1.7-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12rc1-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12rc1-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12rc1-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12rc1-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/Mesquite/Mesquite-2.3.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/Mesquite/Mesquite-2.3.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/Molden/Molden-5.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/Molden/Molden-5.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/__archive__/m/Mono/Mono-2.10.6-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/Mono/Mono-2.10.6-ictce-4.1.13.eb new file mode 100644 index 0000000000000000000000000000000000000000..2971b15c539fff90c884dd0e901d7d48264cee69 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/Mono/Mono-2.10.6-ictce-4.1.13.eb @@ -0,0 +1,28 @@ +name = 'Mono' +version = '2.10.6' + +homepage = 'http://mono-framework.com' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +# Mono required Mono to build, so there are a couple of options: +# 1) provide Mono RPMs in sources, the Mono easyblock will use them to make a tmp Mono install +# 2) assume a Mono version is available system-wide (assert using e.g. "osdependencies = ['mono-core']") +# 3) specify an already available Mono module as build dep, e.g. "builddependencies = [('Mono', '2.10.6')] + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [ + SOURCELOWER_TAR_BZ2, + # Mono requires Mono to build, so provide RPMs so Mono can be bootstrapped + 'libgdiplus-2.4.2-2.el5.kb.x86_64.rpm', + 'mono-core-2.4.2.3-2.el5.kb.x86_64.rpm', +] + +builddependencies = [ + ('Bison', '2.7'), + ('gettext', '0.18.2'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.30.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/Mothur/Mothur-1.30.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/Mothur/Mothur-1.30.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/Mothur/Mothur-1.30.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.1.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.1.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.1.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.1.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MrBayes/MrBayes-3.2.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/__archive__/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb new file mode 100644 index 0000000000000000000000000000000000000000..21917e5c286bf29d77a1e9f38eee5486581d0b1e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.10' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://www.mymedialite.net/download/'] +sources = ['%(name)s-%(version)s.src.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.1.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.1.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.1.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.1.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.1.1-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.1.1-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.1.1-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.1.1-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.0-ictce-4.1.13-Python-2.7.3.eb 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b/easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.12-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/PCRE/PCRE-8.12-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/__archive__/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb similarity index 100% rename from easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb rename to easybuild/easyconfigs/__archive__/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb similarity index 100% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb rename to easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b4-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb b/easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb similarity index 100% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb rename to easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.2.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.2.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb similarity index 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b/easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/ParMGridGen/ParMGridGen-1.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb similarity index 100% rename from easybuild/easyconfigs/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb rename to easybuild/easyconfigs/__archive__/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb similarity index 100% rename from easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb rename to easybuild/easyconfigs/__archive__/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.16.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/Perl/Perl-5.16.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb similarity index 100% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb rename to easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb similarity index 100% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb rename to easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb similarity index 100% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb rename to easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb similarity index 100% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb rename to easybuild/easyconfigs/__archive__/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 458773a19ca69818f02788b8168b4ff2f5a57a47..1837c2a90e23ec6328d37cd45137e3fb97f2e81c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 8847eb716ad958585a1462cfcb3ec0db21ebebe6..9adcb16dd0fc05a77e923a342ed18bedfc3ff1ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index 8721ba5f0a86b47f2fdf5f236aff04191d94a232..9f64cf9e3237cd1869bfb785b23bded1921a50d9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgoolf-1.1.7.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index feaf2e76ec9ca818190b34aaecaaec25d2218eef..6c61e020b76192652e5907d7579e9a264eafce83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmpolf-1.4.8.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 6bbc4316af7a2b38bf3d93880231785261eeffac..f07bce51dbc748781170f077a5ef09adf7ed96b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmvolf-1.7.12.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index b6713093818a55f660b79e0b7873fd7df3022900..0b81650489c035518cbf5497e2f5fa209ac7cf0d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index 383cedbc17d57cd3bcaa0b3a4cc203339e136edd..0bca041c4cdcb33531daf1e1befa009a7c24c688 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index ffaa43d1efacaaeae03cb1dedd1577162ee8e491..a72f677c7d601f885c894f1f604088dffada4bf0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-ictce-4.0.6.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-ictce-4.0.6.eb index 04f049367bdf4021f4ec2af45a36eff04b7ec65f..0b9eaa28a264b77f694cb4f6626c3f285526b754 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-ictce-4.1.13.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-ictce-4.1.13.eb index f3c7ccd43d50161b87fd57ee4b714764222ddc6c..31b3323fc1338df35714284487f597d3701bd5b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iomkl-4.6.13.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iomkl-4.6.13.eb index b36520e7e8afa0caf010275b25d8ff45e39b3f9c..367298ed3a8ae45572aea1cfcd8154768e766da3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iqacml-3.7.3.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 3806ea6dd78b1b3109b836f1bb8a9c3e28317f9a..32d54215536815ab148f0438c2dc77edaa8d613a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index e8290ac41a316a88efeea8c17847b1901f087e3c..ad8c5d831799084ffbe388266c19c165979f3dd4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-ictce-4.1.13.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-ictce-4.1.13.eb index 45b1ca6a64852bde6f903be6922666582a7f6781..648ac1994a619e0f9b669ad1b52222402d438870 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-iqacml-3.7.3.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-iqacml-3.7.3.eb index f5d6db6b40e4e6eb5965e35ca940e59d79e76e00..09835cdeb7bee91e99dc9c5a66810751d9bc7741 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -62,7 +62,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.6-ictce-4.1.13.eb similarity index 97% rename from easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.6-ictce-4.1.13.eb index 146417325f9f850b95a15e73de92e783b47a9cb3..d289934164516bc5b8b1af49806bd4cff549e2be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.19.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb similarity index 96% rename from easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 9282981b3f706b4a8a9172b3f5568c45db80f26d..ae3c7ddc7a7ccc0d2f636873ff6b0ee8bfbf5d99 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-3.2.3-ictce-4.0.6.eb similarity index 96% rename from easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-3.2.3-ictce-4.0.6.eb index b110143efd89ed1e7c341ca56f0d529cf1647d6d..f10e1b0d7d98fd23dba9acd386f59ae5519b5617 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-3.3.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-3.3.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/packmol/packmol-13.243-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/packmol/packmol-13.243-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from 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b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5-ictce-4.1.13-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.5-ictce-4.1.13-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.5-ictce-4.1.13-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.5-ictce-4.1.13-dmpar.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.3.1-ictce-3.2.2.u3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.3.1-ictce-3.2.2.u3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.3.1-ictce-3.2.2.u3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.3.1-ictce-3.2.2.u3-dmpar.eb diff 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a/easybuild/easyconfigs/w/WRF/WRF-3.5-ictce-4.1.13-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.5-ictce-4.1.13-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.5-ictce-4.1.13-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.5-ictce-4.1.13-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.5.1-ictce-4.1.13-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.5.1-ictce-4.1.13-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.5.1-ictce-4.1.13-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.5.1-ictce-4.1.13-dmpar.eb diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0018-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0018-ictce-4.1.13-Perl-5.16.3.eb similarity index 100% rename from easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0018-ictce-4.1.13-Perl-5.16.3.eb rename to easybuild/easyconfigs/__archive__/x/XML-LibXML/XML-LibXML-2.0018-ictce-4.1.13-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/x/XML-Simple/XML-Simple-2.20-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/x/XML-Simple/XML-Simple-2.20-ictce-4.1.13-Perl-5.16.3.eb similarity index 100% rename from easybuild/easyconfigs/x/XML-Simple/XML-Simple-2.20-ictce-4.1.13-Perl-5.16.3.eb rename to easybuild/easyconfigs/__archive__/x/XML-Simple/XML-Simple-2.20-ictce-4.1.13-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb b/easybuild/easyconfigs/__archive__/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb similarity index 100% rename from easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb rename to easybuild/easyconfigs/__archive__/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb b/easybuild/easyconfigs/__archive__/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb similarity index 100% rename from easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb rename to easybuild/easyconfigs/__archive__/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.17-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.17-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.17-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.17-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.17-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/x/xorg-macros/xorg-macros-1.17-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.23-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.23-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.23-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/x/xproto/xproto-7.0.23-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/x/xtrans/xtrans-1.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/x/xtrans/xtrans-1.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb similarity index 72% rename from easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb rename to easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index 814139aaa0a11e22b1788e690bfef34bbb42d813..5efafeb0f0b7058b25a3a189e61f88fcd24a9bea 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -11,6 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. @@ -21,21 +22,15 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['http://www.cpan.org/modules/by-module/YAML'] sources = [SOURCE_TAR_GZ] -perl = 'Perl' -perlver = '5.16.3' -perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) - dependencies = [ - (perl, perlver, perlverextra), + ('Perl', '5.16.3'), ] options = {'modulename': 'YAML::Syck'} -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/YAML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YamCha/YamCha-0.33-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/y/YamCha/YamCha-0.33-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/y/YamCha/YamCha-0.33-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/y/YamCha/YamCha-0.33-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/y/YamCha/YamCha-0.33-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/y/YamCha/YamCha-0.33-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/y/YamCha/YamCha-0.33-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/y/YamCha/YamCha-0.33-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.10.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.10.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.10.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.10.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-6.3.5.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-6.3.5.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zsh/zsh-5.0.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zsh/zsh-5.0.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-intel-2016b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e7c671066207276a325b5b416e43ed21abea489 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '8.0.8b' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abc9e303bfa7f9f43f95598f87d84d5d'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '3.0.0'), + ('netCDF', '4.4.1'), + ('netCDF-Fortran', '4.4.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb b/easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ac6f4932fffa87c627d1fc1c08fd830ae6413a0a --- /dev/null +++ b/easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ART' +version = '2016.06.05' + +homepage = 'http://www.niehs.nih.gov/research/resources/software/biostatistics/art/' +description = "ART is a set of simulation tools to generate synthetic next-generation sequencing reads" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.niehs.nih.gov/research/resources/assets/docs/'] +sources = ['artsrcmountrainier%slinuxtgz.tgz' % ''.join(version.split('.'))] + +dependencies = [ + ('GSL', '2.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/aln2bed.pl', 'bin/art_454', 'bin/art_illumina', 'bin/art_profiler_454', + 'bin/art_profiler_illumina', 'bin/art_SOLiD', 'bin/combinedAvg.pl', 'bin/empDist.pl', + 'bin/fastqReadAvg.pl', 'bin/map2bed.pl', 'bin/summation.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f7c93a41dbad869c76d149870a8303758a704cf --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.20.0' + +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': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0') +] + +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/ATK/ATK-2.22.0-intel-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b536efda0fa66605eee66e43dfb21e9b1f38469 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-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': 'intel', '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/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d4cb8e99dc36057680c4f952ce8cba85b84a59b --- /dev/null +++ b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -0,0 +1,36 @@ +name = 'ATLAS' +version = '3.10.2' + +homepage = 'http://math-atlas.sourceforge.net' +description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of + the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis + on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear + algebra kernel library.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +source_urls = [ + ('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download'), + 'http://www.netlib.org/lapack/', +] +sources = [ + '%(namelower)s%(version)s.tar.bz2', + 'lapack-%s.tgz' % lapackver, +] + +# build full LAPACK library with supplied netlib LAPACK +full_lapack = True + +# fix for http://math-atlas.sourceforge.net/errata.html#sharedProbe +configopts = "-Ss f77lib '-L$(EBROOTGCC)/lib64 -lgfortran'" + +# ignore check done by ATLAS for CPU throttling; +# you should set this to False (or remove it) +# and disable CPU throttling (requires root privileges) if you can +ignorethrottling = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb new file mode 100644 index 0000000000000000000000000000000000000000..89c1628d395b30626ff9dc2e53c1d3053854177d --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -0,0 +1,21 @@ +name = 'Advisor' +version = '2017_update1' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['advisor_%(version)s.tar.gz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..4e451954c3f1494e862623f8d2135b3e5dcf8c38 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb @@ -0,0 +1,29 @@ +name = 'Amber' +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]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'usempi': False} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +patches = ['Amber-%(version)s_fix-hardcoding.patch'] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000000000000000000000000000000000..f910ba5400d6490aaea890df7a1c04778556fc3e --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb @@ -0,0 +1,29 @@ +name = 'Amber' +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]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'usempi': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +patches = ['Amber-%(version)s_fix-hardcoding.patch'] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000000000000000000000000000000000..1b29f57d52d51cbed31bce2236f58f3d5e8f7f9d --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -0,0 +1,32 @@ +name = 'Amber' +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]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'usempi': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +patches = ['Amber-%(version)s_fix-hardcoding.patch', + 'Amber-%(version)s_test_cuda.patch'] + + +dependencies = [ + ('CUDA', '7.5.18', '', True), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch b/easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch new file mode 100644 index 0000000000000000000000000000000000000000..a9b3ba53283254db3fda0f0bf7104cc2c360cdc2 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch @@ -0,0 +1,117 @@ +diff -ur 16-iomkl-2016.09-patchlevel-14-5-serial/AmberTools/src/configure2 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/configure2 +--- 16-iomkl-2016.09-patchlevel-14-5-serial/AmberTools/src/configure2 2016-10-06 14:27:01.000000000 +0100 ++++ 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/configure2 2016-10-06 14:52:11.607328298 +0100 +@@ -513,6 +513,7 @@ + mpi='no' + mtkpp='install_mtkpp' + netcdf_dir='' ++netcdf_fort_dir='' + netcdf_flag='' + netcdfstatic='no' + pnetcdf_dir='' +@@ -587,6 +588,7 @@ + --skip-python) skippython='yes' ;; + --with-python) shift; python="$1";; + --with-netcdf) shift; netcdf_dir="$1";; ++ --with-netcdf-fort) shift; netcdf_fort_dir="$1";; + --with-pnetcdf) shift; pnetcdf_dir="$1" ;; + --python-install) shift; python_install="$1";; + -netcdfstatic) netcdfstatic='yes' ;; +@@ -778,7 +780,7 @@ + flibsf="-larpack -llapack -lblas" + # only used when the user requests a static build or when a static build is + # automatically set, eg, windows: +-staticflag='-static' ++staticflag='-static-intel' + omp_flag= + mpi_flag= + fp_flags= +@@ -1280,7 +1282,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1598,7 +1600,7 @@ + fi + + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1924,7 +1926,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2059,7 +2061,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2131,17 +2133,17 @@ + blas=skip + flibs="-larpack " + flibsf="-larpack " +- mkll="$MKL_HOME/lib/32" ++ mkll="$MKL_HOME/mkl/lib/32" + mkl_processor="32" + mkl_procstring="ia32" + mklinterfacelayer='libmkl_intel.a' + if [ "$x86_64" = 'yes' ]; then +- if [ -d "$MKL_HOME/lib/em64t" ]; then +- mkll="$MKL_HOME/lib/em64t" ++ if [ -d "$MKL_HOME/mkl/lib/em64t" ]; then ++ mkll="$MKL_HOME/mkl/lib/em64t" + mkl_processor="em64t" + mkl_procstring="em64t" + else +- mkll="$MKL_HOME/lib/intel64" ++ mkll="$MKL_HOME/mkl/lib/intel64" + mkl_processor="intel64" + mkl_procstring="intel64" + fi +@@ -2567,11 +2569,16 @@ + else + # A NetCDF directory was specified. Check that library exists and compiles + printf "\tUsing external NetCDF in '$netcdf_dir'\n" ++ # Support separate NetCDF-Fortran installation with --with-netcdf-fort ++ if [ ! -e "$netcdf_fort_dir" ]; then ++ netcdf_fort_dir="$netcdf_dir" ++ fi ++ printf "\tUsing external NetCDF-Fortran in '$netcdf_fort_dir'\n" + netcdfinc="-I"$netcdf_dir"/include" + if [ "${netcdf_dir}" != '/usr' -a "$netcdf_dir" != '/usr/' ]; then + netcdf_flag="-L${netcdf_dir}/lib $netcdf_flag" + fi +- netcdf=$netcdf_dir"/include/netcdf.mod" ++ netcdf=$netcdf_fort_dir"/include/netcdf.mod" + if [ "$netcdfstatic" = 'no' ] ; then + if [ "${netcdf_dir}" != '/usr' -a "${netcdf_dir}" != '/usr/' ]; then + netcdfflagc="-L${netcdf_dir}/lib -lnetcdf" +@@ -2587,7 +2594,7 @@ + echo "Error: '$netcdfflagc' not found." + exit 1 + fi +- netcdfflagf=$netcdf_dir"/lib/libnetcdff.a" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff.a" + if [ ! -e "$netcdfflagf" ]; then + echo "Error: '$netcdfflagf' not found." + exit 1 +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src: configure2.orig +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src: configure2.rej +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/cpptraj: configure.orig +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/cpptraj: configure.rej diff --git a/easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch b/easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch new file mode 100644 index 0000000000000000000000000000000000000000..6b4af61766f891b81848bafd843fa1c29ba8fa3d --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch @@ -0,0 +1,13 @@ +--- Makefile.orig 2016-10-14 10:17:32.020437000 +0100 ++++ Makefile 2016-10-14 10:18:12.940992000 +0100 +@@ -80,6 +80,10 @@ + fi ;\ + ) + ++test.cuda: ++ # For backwards compatibility in the easyblock ++ -(cd test && $(MAKE) test.cuda.serial) ++ + test.cuda_serial: + -(cd test && $(MAKE) test.cuda.serial) + diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..c0ff978ea57c40c5c71d57c01576ba6ad878bd60 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -0,0 +1,23 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda2' +version = '4.0.0' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['31ed3ef07435d7068e1e03be49381b13'] + +# a newer version of conda is required to run 'conda env create -p' +prep_env = "PATH=%(installdir)s/bin:$PATH " +postinstallcmds = [prep_env + "conda install -f -p %(installdir)s -c conda conda=4.2.12 ruamel_yaml=0.11.14"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..87325e0a063e739e8db1782849d3c393794d7fb1 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -0,0 +1,23 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '4.0.0' + +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 = ['http://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['546d1f02597587c685fa890c1d713b51'] + +# a newer version of conda is required to run 'conda env create -p' +prep_env = "PATH=%(installdir)s/bin:$PATH " +postinstallcmds = [prep_env + "conda install -f -p %(installdir)s -c conda conda=4.2.12 ruamel_yaml=0.11.14"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..94bbfc01ec2e0abd18803ff63fe08a9a345e1d4f --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.eb @@ -0,0 +1,26 @@ +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': '2016.04'} + +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-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..463a75eb42c6074742bd43d6f4e93750e53d3b80 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.07.eb @@ -0,0 +1,26 @@ +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': 'iomkl', 'version': '2016.07'} + +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..f88254bccf6442beeed7ed178c0681ce02ca573c --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..40213b047b74a203dfbb4fa6e04d5b8bdd7ddda8 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.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': '2016.04'} + +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/Automake/Automake-1.15-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..d787cbd50ba498a1436574c0409e5c5f9efb34c0 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +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/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..c8260533e67f1dd51462723aabea5d7e165a8d51 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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-foss-2016.04.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..05ba2a5c7549c82fdb607570686015ac061b68b5 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016.04.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': '2016.04'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..33124456f6e3e891cfac776d1e1160d272b3156b --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.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': 'intel', 'version': '2015a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..d27dde01f2a61006cb2bfa6719fbb3ac3da3a996 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..1fe6a834c71f9b43736cc34fa668504296431ee1 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..c9d9db6e85f23d4f549a6c88f5345ccf584ee1b9 --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'angsd' +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/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('HTSlib', '1.3.1')] + +files_to_copy = [ + (['angsd'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..939e49dbc0961303a46b95a554b54438144dcb06 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.3.0' + +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': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2016b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..feba2c7b4c9f46e0caccf00c10c43245955d6bfc --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-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': 'intel', '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/atools/atools-1.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/atools/atools-1.4.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f41851d672f5c7b1063a2f5e93282a5991fa823 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.4.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gjbex/atools/archive'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/aenv', 'bin/alog', 'bin/arange'], + 'dirs': ['lib/vsc/atools'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ce1d7a97a912706d3010bb946f390691714aa3df --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'awscli' +version = '1.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'intel', '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-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 new file mode 100644 index 0000000000000000000000000000000000000000..539e3c2d208966150d41c119bd2662d4d21d03b9 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '36.62' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://sourceforge.net/projects/bbmap/' +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' ] + +dependencies = [('Java', '1.8.0_112', '', True)] + +prebuildopts = 'cd jni && ' + +suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh'], + 'dirs': [] +} + +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.""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bbeac455b9cc5b1467ec6f9b148b4b2abac4089 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb @@ -0,0 +1,27 @@ +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'BEDOPS' +version = '2.4.20' + +homepage = 'http://bedops.readthedocs.io/en/latest/index.html' +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient + and scalable Boolean and other set operations, statistical calculations, archiving, conversion + and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome + for distributing whole-genome analyses across a computational cluster.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = ['%(namelower)s_linux_x86_64-v%(version)s.v2.tar.bz2'] +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] + +sanity_check_paths = { + 'files': ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'], + 'dirs': ['.'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb b/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..714b83985a39f8ce0e43bbdfa3c119ee5e1ed71b --- /dev/null +++ b/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb @@ -0,0 +1,24 @@ +name = 'BLACS' +version = '1.1' + +homepage = 'http://www.netlib.org/blacs/' +description = """The BLACS (Basic Linear Algebra Communication Subprograms) project is + an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface + that may be implemented efficiently and uniformly across a large range of distributed memory platforms.""" + +toolchain = {'name': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [ + 'mpiblacs.tgz', + 'mpiblacs-patch03.tgz', +] +checksums = [ + '28ae5b91b3193402fe1ae8d06adcf500', + '48fdf5e4ef6cf53daec9eeef40498a8b', +] + +patches = ['bmake.mpi.patch'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb index 22babb46e9e36ae27d48862030dd750426baad55..5befdd3e111e267098d9357072100d900de5a494 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = "Tarball" +easyblock = 'Tarball' name = 'BLAST' version = '2.2.26' @@ -16,7 +16,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version)s/'] +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast//executables/legacy/%(version)s/'] sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..62b042ace97e45a63ef7992c67fdeb42f806e444 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb @@ -0,0 +1,32 @@ +## +# 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 +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.15' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b1a2aa0cf6716a1ac261201c8f1ce087928acd37 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , George Tsouloupas +# License:: MIT/GPL +# +## + +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': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '3.4.3')] + +files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"] + +sanity_check_paths = { + 'files': ["bin/bamtools", "include/shared/bamtools_global.h", "lib/libbamtools.a", + "lib/libbamtools.so", "lib/libbamtools-utils.a", "lib/libjsoncpp.a"], + 'dirs': ["include/api", "docs"] +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..e948c06e11a279562b5b09a1b6b78bb55c0e28aa --- /dev/null +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayPass' +version = '2.1' + +homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html' +description = """BayPass is a population genomics software which is primarily aimed at identifying + genetic markers subjected to selection and/or associated to population-specific covariates + (e.g., environmental variables, quantitative or categorical phenotypic characteristics). + The underlying models explicitly account for (and may estimate) the covariance structure among the + population allele frequencies that originates from the shared history of the populations under study""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/baypass/files/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +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' +] + +sanity_check_paths = { + 'files': ['bin/g_baypass'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c4932d395387365c8aea6d9def5215cb012e01f5 --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -0,0 +1,39 @@ +# 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 = 'BayeScan' +version = '2.1' + +homepage = 'http://cmpg.unibe.ch/software/BayeScan/' +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, + using differences in allele frequencies between populations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/'] +sources = ['%(name)s%(version)s.zip'] + +prebuildopts = "sed -i.bk 's/g++/${CXX} ${CXXFLAGS}/g' Makefile && " + +start_dir = 'source' + +files_to_copy = [ + (['source/bayescan_%(version)s'], 'bin'), + 'BayeScan%(version)s_manual.pdf', + 'input_examples', + 'R functions' +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescan_%(version)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..4a78852736c7f1f4f99e3fe097753c0438d2894e --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-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 = '1.7.0' +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': 'foss', '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/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 new file mode 100644 index 0000000000000000000000000000000000000000..1c5fd3f356ca289c9b3e2e51c73432d62d9d8f1f --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,41 @@ +## +# 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 +# +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.68' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..953304846ea999c7fea3c7769546c37127498be3 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.68' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..b22f51705c3c532edd50b5307bd25febb98e5ea7 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.68' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..59b38bba21849b6651b93e9cce0006fabff68b71 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb @@ -0,0 +1,26 @@ +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': '6.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # 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-iomkl-2016.07.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..0027e83817bbce65a53cbcddf6ae1ed26f83a2da --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.07.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..31858dc8f252b91581b9ddd449c0aa76ad754375 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..1ddf498f76a50c8d06bc03440c28867abbb6e700 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'Blender' +version = '2.77a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://download.blender.org/source/'] +patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] + +# disable SSE detection to give EasyBuild full control over optimization compiler flags being used +configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' + +# these are needed until extra dependencies are added for them to work +configopts += '-DWITH_INSTALL_PORTABLE=OFF ' +configopts += '-DWITH_BUILDINFO=OFF ' +configopts += '-DWITH_GAMEENGINE=OFF ' +configopts += '-DWITH_SYSTEM_GLEW=OFF ' + +# Python paths +configopts += '-DPYTHON_VERSION=%(pyshortver)s -DPYTHON_LIBRARY=${EBROOTPYTHON}/lib/libpython%(pyshortver)sm.so ' +configopts += '-DPYTHON_INCLUDE_DIR=${EBROOTPYTHON}/include/python%(pyshortver)sm ' +configopts += '-DOPENEXR_INCLUDE_DIR=$EBROOTOPENEXR/include ' + +dependencies = [ + ('Python', '3.5.2'), + ('Boost', '1.61.0'), + ('libjpeg-turbo', '1.5.0'), + ('zlib', '1.2.8'), + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('OpenImageIO', '1.6.17'), # required for cycles render engine +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = 'True' + +modextravars = {'GALLIUM_DRIVER': 'swr'} + +sanity_check_paths = { + 'files': ['bin/blender'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch b/easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch new file mode 100644 index 0000000000000000000000000000000000000000..2cc57b24de0ade8d76f1b8624fe1c9c4100d7a45 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch @@ -0,0 +1,13 @@ +use simple definition of ARRAY_SIZE macro when using Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- blender-2.77a/source/blender/blenlib/BLI_utildefines.h.orig 2016-09-07 14:21:00.287130174 +0200 ++++ blender-2.77a/source/blender/blenlib/BLI_utildefines.h 2016-09-07 14:21:08.087031653 +0200 +@@ -435,7 +435,7 @@ + } (void)0 + + /* assuming a static array */ +-#if defined(__GNUC__) && !defined(__cplusplus) && !defined(__clang__) ++#if defined(__GNUC__) && !defined(__cplusplus) && !defined(__clang__) && !defined(__INTEL_COMPILER) + # define ARRAY_SIZE(arr) \ + ((sizeof(struct {int isnt_array : ((const void *)&(arr) == &(arr)[0]);}) * 0) + \ + (sizeof(arr) / sizeof(*(arr)))) diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..088b4857b51c695ef54ce6911485c8db13a4c5de --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.11.1' + +homepage = 'http://www.blosc.org/' +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.6.2')] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..a0f2183ed366bdb6783524df778af5c106854c7d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +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-1.61.0-foss-2016b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..876bfa42e6c1bd11ef7656a9540ddd363fa83212 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..67f6199614993f617b8c8a36636507a06b2e09e1 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index f54d71284a0c2819be918438a6c9390388fe7dba..eba16d5a4e38c16f2bcb94fb6288401e45c13c32 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -18,6 +18,8 @@ sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] +builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] + patches = ['beagle-lib-20120124_GCC-4.7.patch'] # parallel build does not work diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index d4fc0c8fee561bf2c77355aa43b26c92242d14a8..6d20b44133fec89041207b86e3a6c2df71c9730b 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -16,6 +16,8 @@ sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] +builddependencies = [('Autotools', '20150215')] + # parallel build does not work parallel = 1 diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index cc7febf444602efa1700606a61d32d29d50923b5..0349d94e2ac9283eacf087310ae65effc162da30 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -15,10 +15,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [ - ('Java', '1.8.0_31', '', True), - ('Autoconf', '2.69') -] +dependencies = [('Java', '1.8.0_31', '', True)] +builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..515ba57589288ff1f25c2596cf3cbbbd516db23a --- /dev/null +++ b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'behave' +version = '1.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pythonhosted.org/behave' +description = """behave: Behavior-driven development (or BDD) is an +agile software development technique that encourages collaboration +between developers, QA and non-technical or business participants in a +software project.""" + +toolchain = {'name': 'foss', '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 = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 7598e76c0730b11c331fb482479d25903de038e8..2c7152bf011aacf8978bb276c7ce7461535debb4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -13,6 +13,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# libiberty doesn't seem to compile with Intel compilers +install_libiberty = False + # disable warning/error #175 ("subscript out of range") buildopts = 'CFLAGS="$CFLAGS -wd175"' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..215aaf0cb28f0364da4319477845fbc91b712779 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.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': '6.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), + # 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/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa1cb3dc2c81fa935c96d076dedbb761db1e9399 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'bokeh' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('PyYAML', '3.12', versionsuffix), +] + +exts_list = [ + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('requests', '2.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], + }), +] + +# 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/bokeh', 'bin/bokeh-server'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..84e9ec4ffb6b27371a3337dff29763e07a0289c5 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'bokeh' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('PyYAML', '3.12', versionsuffix), +] + +exts_list = [ + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('requests', '2.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], + }), +] + +# 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/bokeh', 'bin/bokeh-server'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e016d4b0dc399d14b9995b043dae476c2b80e10 --- /dev/null +++ b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.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 = 'Tarball' + +name = 'bwakit' +version = '0.7.15' +versionsuffix = '_x64-linux' + +homepage = 'https://github.com/lh3/bwa/tree/master/bwakit' +description = """Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, +providing an end-to-end solution to read mapping.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://sourceforge.net/projects/bio-bwa/files/bwakit/'] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.bz2'] + +sanity_check_paths = { + 'files': ['bwa', 'samtools'], + 'dirs': [] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a99a45a08583466923ad43b0a994ab877a3f824 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb @@ -0,0 +1,15 @@ +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': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..deec24c55d0c2fe85648d2e06b774b4525ae90ac --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb @@ -0,0 +1,16 @@ +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..6ad5b69ca60c38c1a97d6a395bc666d843217998 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb @@ -0,0 +1,15 @@ +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..d16cac5f5dca4c2154b6acb02c9f382910783588 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,15 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..aadc3712b462532f376dc137904ed540f806d301 --- /dev/null +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb @@ -0,0 +1,22 @@ +name = 'CBLAS' +version = '20110120' + +homepage = 'http://www.netlib.org/blas/' +description = "C interface to the BLAS" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/blas/blast-forum/'] +sources = ['cblas.tgz'] + +patches = ['CBLAS_shared-lib.patch'] + +buildopts = 'all shared' + +# parallel build fails occasionally +parallel = 1 + +runtest = 'runtst' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.7.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..3af830a1e641cd80e4f7e88e15a814e281b285bf --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.7.2-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.7.2' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://code.zmaw.de/attachments/download/12760/'] +checksums = [('md5', 'f08e4ce8739a4f2b63fc81a24db3ee31')] + +dependencies = [ + ('HDF5', '1.8.17'), + ('netCDF', '4.4.1'), + ('YAXT', '0.5.1'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" + +sanity_check_paths = { + 'files': ["bin/cdo"], + 'dirs': [], +} + +moduleclass = 'data' 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 new file mode 100755 index 0000000000000000000000000000000000000000..8c90ec640b0236d20dc1748b65d5070891dd4ed2 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.300' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +srcversion = version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/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-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..3efaca57eb38ef9ca38118ac3b13686b7e14c400 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-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': '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', '1.61.0', 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=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..406b208a885a64eb4cf6c8adf3ab4054ce1af3c5 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb @@ -0,0 +1,34 @@ +name = 'CGAL' +version = '4.8.1' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Boost', '1.61.0'), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Eigen', '3.2.9'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$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/CMake/CMake-3.4.1-iomkl-2016.07.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..0204c038c79b1d9b90acf1cda613239af202f760 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +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': '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' + +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'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/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 new file mode 100644 index 0000000000000000000000000000000000000000..36a239c230c516bd3d7d7e5f31748393b84686b2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +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': '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' + +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'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cfb29da8c6bf080ad09d850d55b07d4ee2204841 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.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': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..adb0724437a111d40b93466730dc87eb11286f72 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6e496837c29857c60970db220b2ab962dae18e0 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..eecde070965c12d94cf445a9491fe5aefe223fb5 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University, Microway +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste, Eliot Eshelman +# 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_2012-99.html +## + +name = 'CUDA' +version = '7.5.18' + +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': 'GCC', 'version': '4.9.4-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] + +# Necessary to allow to use a GCC 4.9.4 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems +installopts = '-override compiler' + +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 new file mode 100644 index 0000000000000000000000000000000000000000..8ed8a29bfcb7c7cb6ce0e1d4d2fc6eaf397f6e7d --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.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, Ghent University, +# Forschungszentrum Juelich +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# Authors:: Damian Alvarez +# 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_2012-99.html +## + +#easyblock = 'ConfigureMake' + +name = 'CUDA' +version = '7.5.18' + +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': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] + +# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems +installopts = '-override compiler' + +host_compilers = ["icpc", "g++"] + +# Be careful and have a message consistent with the generated wrappers +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..414d7ab0924100562aa54f470e9b3a220fb03c7a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb @@ -0,0 +1,19 @@ +name = 'CUDA' +version = '8.0.44' + +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': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/', + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/' +] + +sources = ['%(namelower)s_%(version)s_linux-run'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..c0dc1eccdc210292401c9938e5e4cc34f11a9850 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,19 @@ +name = 'CUDA' +version = '8.0.44' + +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': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/', + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/' +] + +sources = ['%(namelower)s_%(version)s_linux-run'] + +moduleclass = 'system' 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 new file mode 100644 index 0000000000000000000000000000000000000000..df2115bf2e20534ea02b491090e5877b22060915 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,41 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.61.0', versionsuffix), + ('SUNDIALS', '2.6.2'), +] +builddependencies = [ + ('SCons', '2.5.0', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + common_opts +runtest = 'test ' + common_opts +buildopts = 'install ' + common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mixmaster'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb b/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc872af329740fd6a26b2767fb61f46d975b0998 --- /dev/null +++ b/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Cargo' +version = '0.13.0' + +homepage = 'https://crates.io/' +description = "The Rust package manager" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'https://github.com/rust-lang/cargo/archive/', + 'https://github.com/rust-lang/rust-installer/archive/', +] +sources = [ + '%(version)s.tar.gz', + '4f99485.tar.gz', # rust-installer +] + +dependencies = [ + ('Rust', '1.12.1'), +] +builddependencies = [ + ('CMake', '3.6.2'), + ('Python', '2.7.12'), + ('cURL', '7.49.1'), +] + +buildopts = 'VERBOSE=1' +# rust-installer is a git submodule, but not included in the sources pulled from GitHub +# see also https://github.com/rust-lang/cargo/issues/2130 +preinstallopts = "cp -a %(builddir)s/rust-installer*/* %(builddir)s/cargo-%(version)s/src/rust-installer && " + +sanity_check_paths = { + 'files': ['bin/cargo'], + 'dirs': ['etc', 'lib/rustlib', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a03b23888fb7ac04a2adb1bd26f3cc7a9c83d8c --- /dev/null +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb @@ -0,0 +1,35 @@ +## +# 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 +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ClustalW2' +version = '2.1' + +homepage = 'http://www.ebi.ac.uk/Tools/msa/clustalw2/' +description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.clustal.org/download/%(version)s'] +sources = ['clustalw-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/clustalw2'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7cce1f35188b0aca02b3698cd0bb5aa670f9b2a5 --- /dev/null +++ b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,81 @@ +# 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 = 'Cookiecutter' +version = '1.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/audreyr/cookiecutter' +description = """Command-line utility that creates projects from cookiecutters (project templates). + E.g. Python package projects, jQuery plugin projects.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), +] + +# this application also requires numpy, scipy and matplotlib which +# are provided by the Python module +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-dateutil', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('future', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], + }), + ('whichcraft', '0.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/w/whichcraft/'], + }), + ('arrow', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/arrow/'], + }), + ('chardet', '2.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + }), + ('binaryornot', '0.4.0', { + 'source_urls': ['https://pypi.io/packages/source/b/binaryornot/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jinja2-time', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jinja2-time/'], + 'modulename': 'jinja2', + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('poyo', '0.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/poyo/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + }), + ('cookiecutter', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cookiecutter/'], + }), +] + +# 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/%s' % x for x in ['chardetect', 'cookiecutter', 'futurize', 'pasteurize']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..94f4a3ca61d3d4f4d7f3e3885f4c23b2e37f91a4 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Cube' +version = '4.2' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +# Backported fixes included in Cube 4.2.2 and up +patches = [ + 'Cube-%(version)s_fix-Qt-version-check.patch', + 'Cube-%(version)s_fix-with-qt-check.patch', +] + +checksums = [ + 'aa1b1594bacddd3a1931f9a9dea23ce8', # cube-4.2.tar.gz + 'da69fe49d347dc7722c30bb785106d96', # Cube-4.2_fix-Qt-version-check.patch + '5a746d4f6f4eb5eb8b464ca355b46891', # Cube-4.2_fix-with-qt-check.patch +] + +dependencies = [('Qt', '4.8.6')] + +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support has difficulties handling +# parallel builds. +configopts = '--without-java-reader' + +sanity_check_paths = { + 'files': ['bin/cube', ('lib/libcube4.a', 'lib64/libcube4.a'), + ('lib/libcube4.%s' % SHLIB_EXT, 'lib64/libcube4.%s' % SHLIB_EXT)], + 'dirs': ['include/cube', 'include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2016b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5337cc8919d9220307937eb06810a57db3cec417 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2016b.eb @@ -0,0 +1,28 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.61.0', '-Python-2.7.12'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.3'), + ('zlib', '1.2.8'), +] + +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a2db0bddbe99132238a4d27f2a5214262a4b4899 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.24.1' +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': [cythonlibdir + '/%(name)s'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..85d8a324484c935e8e649ee282aadc1f96f08044 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.46.0' + +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': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# 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-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa8f0b1dc211f68a7a050445e08221e302089fd4 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.46.0' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..54967b2ef70805d4d9d341bf993395122c43711e --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$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/ccache/ccache-3.3.1.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..66a9fe225ab7cd620e3562b0a4e585681e64249c --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.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 +# $Id$ +## +easyblock = 'ConfigureMake' + +name = 'ccache' +version = '3.3.1' + +homepage = 'http://ccache.samba.org/' +description = """ccache-3.1.9: Cache for C/C++ compilers""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'static': True} + +source_urls = ['https://github.com/ccache/ccache/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Autotools', '20150215'), + ('zlib', '1.2.8'), +] + +preconfigopts = "./autogen.sh && " +buildopts = 'LDFLAGS="-static"' + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..f3c8b6240f9df14e1034a58ba9c12087b5a305a4 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.3.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 +# $Id$ +## +easyblock = 'ConfigureMake' + +name = 'ccache' +version = '3.3.3' + +homepage = 'http://ccache.samba.org/' +description = """ccache-3.1.9: Cache for C/C++ compilers""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'static': True} + +source_urls = ['https://github.com/ccache/ccache/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Autotools', '20150215'), + ('zlib', '1.2.8'), +] + +preconfigopts = "./autogen.sh && " +buildopts = 'LDFLAGS="-static"' + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000000000000000000000000000000000..e3bb6d9e200c45ba9bcb91880a3672f3896906db --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,32 @@ +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': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] +sources = ['configparser-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.5.2'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('python', "-c 'import configparser'"), + ('python', "-c 'from backports import configparser'"), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb b/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..70ed0f8ae7e86b7b65a1d736fb61ef0905d67da0 --- /dev/null +++ b/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb @@ -0,0 +1,23 @@ +name = 'cppcheck' +version = '1.75' + +homepage = 'http://cppcheck.sourceforge.net/' +description = """Cppcheck is a static analysis tool for C/C++ code""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [ + ('Qt5', '5.5.1'), + ('PCRE', '8.37'), +] + +have_rules = True +build_gui = True + +buildopts = 'CXXFLAGS="$CXXFLAGS -std=c++11"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a65c07d0ff3d66afb68c94c5c8f90fe9512b0a6 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.033' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/C/CA/CAPTTOFU/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.24.0'), + ('MariaDB', '10.1.17'), + ('zlib', '1.2.8'), + # OS dependency should be preferred if the os version is more recent then this version + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1q'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# force static linking of libmysqlclient to dance around problem with unresolved symbols +configopts = '--libs="-L$EBROOTMARIADB/lib -Wl,-Bstatic -lmysqlclient -Wl,-Bdynamic -lpthread -lz -lrt -lssl -lcrypto"' + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql'], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..7071afdb2c399a237e3b67f396969e2547ad2fd5 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.12' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +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']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..0940c66fb5b827ec733ab871720e5d2598efe97f --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.8' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +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']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-foss-2015b-PLUMED-2.1.4.eb b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-foss-2015b-PLUMED-2.1.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..72b577354664eb748cc36a7de1454837f316a2ce --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-foss-2015b-PLUMED-2.1.4.eb @@ -0,0 +1,32 @@ +name = 'DL_POLY_Classic' +version = '1.9' + +homepage = 'http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/' +description = """DL_POLY Classic is a freely available molecular dynamics program developed + from the DL_POLY_2 package. This version does not install the java gui.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/255/2627/'] +sources = [ + 'dl_class_%(version)s.tar.gz', + # download from https://groups.google.com/group/plumed-users/attach/85c9fdc16956d/dlpoly2.tar.gz?part=0.1&authuser=0 + # see https://groups.google.com/d/msg/plumed-users/cWaIDU5F6Bw/bZUW3J9cCAAJ + 'dlpoly2.tar.gz', +] +patches = [('DL_POLY_Classic-%(version)s_fix-PLUMED-integration.patch', '..')] +checksums = [ + '66e40eccc6d3f696c8e3654b5dd2de54', # dl_class_1.9.tar.gz + '39edd8805751b3581b9a4a0147ec1c67', # dlpoly2.tar.gz + '81f2cfd95c578aabc5c87a2777b106c3', # DL_POLY_Classic-1.9_fix-PLUMED-integration.patch +] + +plumedversion = '2.1.4' +versionsuffix = '-PLUMED-%s' % plumedversion + +dependencies = [('PLUMED', plumedversion)] + +# parallel build tends to break +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-foss-2015b-PLUMED-2.2.0.eb b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-foss-2015b-PLUMED-2.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e62d26024b036892f2d50025725cc2c90b7d61e4 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-foss-2015b-PLUMED-2.2.0.eb @@ -0,0 +1,32 @@ +name = 'DL_POLY_Classic' +version = '1.9' + +homepage = 'http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/' +description = """DL_POLY Classic is a freely available molecular dynamics program developed + from the DL_POLY_2 package. This version does not install the java gui.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/255/2627/'] +sources = [ + 'dl_class_%(version)s.tar.gz', + # download from https://groups.google.com/group/plumed-users/attach/85c9fdc16956d/dlpoly2.tar.gz?part=0.1&authuser=0 + # see https://groups.google.com/d/msg/plumed-users/cWaIDU5F6Bw/bZUW3J9cCAAJ + 'dlpoly2.tar.gz', +] +patches = [('DL_POLY_Classic-%(version)s_fix-PLUMED-integration.patch', '..')] +checksums = [ + '66e40eccc6d3f696c8e3654b5dd2de54', # dl_class_1.9.tar.gz + '39edd8805751b3581b9a4a0147ec1c67', # dlpoly2.tar.gz + '81f2cfd95c578aabc5c87a2777b106c3', # DL_POLY_Classic-1.9_fix-PLUMED-integration.patch +] + +plumedversion = '2.2.0' +versionsuffix = '-PLUMED-%s' % plumedversion + +dependencies = [('PLUMED', plumedversion)] + +# parallel build tends to break +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-ictce-5.3.0-no-gui.eb b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-ictce-5.3.0-no-gui.eb index a5b0e16996edce176e4a195ea3ef37ad42030f13..daa85f8912eb90ae0df8c33e7c6c21c636647da5 100644 --- a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-ictce-5.3.0-no-gui.eb +++ b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-ictce-5.3.0-no-gui.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['dl_class_%(version)s.tar.gz'] source_urls = ['http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/255/2627/'] +checksums = ['66e40eccc6d3f696c8e3654b5dd2de54'] sanity_check_paths = { 'files': ['bin/DLPOLY.X'], diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-intel-2016b-PLUMED-2.2.3.eb b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-intel-2016b-PLUMED-2.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..0223680bc95d7d9533e03b7745078bb78f782bc7 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-intel-2016b-PLUMED-2.2.3.eb @@ -0,0 +1,33 @@ +name = 'DL_POLY_Classic' +version = '1.9' + +homepage = 'http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/' +description = """DL_POLY Classic is a freely available molecular dynamics program developed + from the DL_POLY_2 package. This version does not install the java gui.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/255/2627/'] +sources = [ + 'dl_class_%(version)s.tar.gz', + # download from https://groups.google.com/group/plumed-users/attach/85c9fdc16956d/dlpoly2.tar.gz?part=0.1&authuser=0 + # see https://groups.google.com/d/msg/plumed-users/cWaIDU5F6Bw/bZUW3J9cCAAJ + 'dlpoly2.tar.gz', +] +patches = [('DL_POLY_Classic-%(version)s_fix-PLUMED-integration.patch', '..')] +checksums = [ + '66e40eccc6d3f696c8e3654b5dd2de54', # dl_class_1.9.tar.gz + '39edd8805751b3581b9a4a0147ec1c67', # dlpoly2.tar.gz + '81f2cfd95c578aabc5c87a2777b106c3', # DL_POLY_Classic-1.9_fix-PLUMED-integration.patch +] + + +plumedversion = '2.2.3' +versionsuffix = '-PLUMED-%s' % plumedversion + +dependencies = [('PLUMED', plumedversion)] + +# parallel build tends to break +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-intel-2016b.eb b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..04e4e4da9bb0f013e41dfeeab2e1d8228c12a83c --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9-intel-2016b.eb @@ -0,0 +1,17 @@ +name = 'DL_POLY_Classic' +version = '1.9' + +homepage = 'http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/' +description = """DL_POLY Classic is a freely available molecular dynamics program developed + from the DL_POLY_2 package. This version does not install the java gui.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['dl_class_%(version)s.tar.gz'] +source_urls = ['http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/255/2627/'] +checksums = ['66e40eccc6d3f696c8e3654b5dd2de54'] + +# parallel build tends to break +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9_fix-PLUMED-integration.patch b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9_fix-PLUMED-integration.patch new file mode 100644 index 0000000000000000000000000000000000000000..550a4ce5fb42489db3f23ee01f7cbcbac64192b1 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic/DL_POLY_Classic-1.9_fix-PLUMED-integration.patch @@ -0,0 +1,1355 @@ +fix patch to make DL_Poly Classic 1.9 work with PLUMED +original patch is obtained as a tarball named dlpoly2.tar.gz from +https://groups.google.com/group/plumed-users/attach/85c9fdc16956d/dlpoly2.tar.gz?part=0.1&authuser=0 +see also https://groups.google.com/d/msg/plumed-users/cWaIDU5F6Bw/bZUW3J9cCAAJ + +author: Kenneth Hoste, Ward Poelmans (HPC-UGent) +--- dlpoly-2.20.diff/srcmod/dlpoly.f.preplumed.orig 2016-11-25 16:52:49.870981815 +0100 ++++ dlpoly-2.20.diff/srcmod/dlpoly.f.preplumed 2016-11-25 16:57:11.720654972 +0100 +@@ -1,21 +1,14 @@ +- program dlpoly ++ program dlpoly_classic + + c*********************************************************************** + c +-c dl_poly is an cclrc/ccp5 program package for the dynamical +-c simulation of molecular systems. ++c dl_poly classic is an stfc/ccp5 program package for the ++c dynamical simulation of molecular systems. + c +-c dl_poly is the property of the cclrc daresbury laboratory, +-c daresbury, warrington wa4 4ad. no part of the package may +-c be redistributed to third parties without the consent of +-c daresbury laboratory. ++c dl_poly is the copyright of the stfc daresbury laboratory, ++c daresbury, warrington wa4 4ad. + c +-c dl_poly is available free of charge to academic institutions +-c engaged in non-commercial research only. potential users not +-c in this category must consult the ccp5 program librarian at +-c daresbury to negotiate terms of use. +-c +-c neither the cclrc, daresbury laboratory, ccp5 nor the authors ++c neither the stfc, daresbury laboratory, ccp5 nor the authors + c of this package claim that it is free from errors and do not + c accept liability for any loss or damage that may arise from + c its use. it is the users responsibility to verify that the +@@ -23,19 +16,13 @@ + c it. + c + c users of this package are recommended to consult the dl_poly +-c user and reference manuals for the full terms and conditions +-c of its use. ++c user manual for the full description of its use and purpose. + c + c authors: w.smith and t.r.forester 1995 + c copyright daresbury laboratory 1995 + c +-c release 2.20 +-c +-c wl +-c 2009/01/15 11:55:48 +-c 1.20 +-c Exp +-c ++c DL_POLY CLASSIC VERSION 1.9 ++c + c*********************************************************************** + + c declare required modules +@@ -57,6 +44,7 @@ + use integrator_module + use inversion_module + use metal_module ++ use metafreeze_module + use nlist_builders_module + use pair_module + use pmf_module +@@ -76,11 +64,14 @@ + + implicit none + ++ character*1 hms,dec ++ character*8 seek ++ + logical ltscal,lzeql,loptim,ltraj,lgofr,lpgr,lfcap,recycle + logical newlst,lneut,loglnk,lnsq,lzden,lshmov,lcnb,ltad,lneb + logical stropt,lzero,nolink,newgau,lminim,lminnow,lhit,lbpd + logical prechk,tadall,lexcite,lsolva,lfree,lfrmas,lswitch +- logical lghost,llswitch ++ logical lghost,llswitch,lnfic,nebgo,lpsoc,redirect + + integer npage,lines,idnode,mxnode,memr,intsta,istraj,nsbzdn + integer keyens,keyfce,keyres,keytrj,kmax1,kmax2,kmax3,multt +@@ -91,7 +82,7 @@ + integer ntteth,ntshl,nstep,numacc,numrdf,nzden,nscons,i,k + integer ntpter,keyshl,isw,keyver,keystr,keytol,numgau,khit + integer nhit,keybpd,ntrack,nblock,blkout,numneb,nturn,mode +- integer natms2,ntghost,nsolva,isolva ++ integer natms2,ntghost,nsolva,isolva,nofic + + real(8) alpha,delr,epsq,fmax,press,quattol,rcut,rprim,rvdw,taup + real(8) taut,temp,timcls,timjob,tolnce,tstep,tzero,dlrpot,drewd +@@ -100,53 +91,44 @@ + real(8) engdih,virdih,enginv,virinv,engtbp,virtbp,engter,virter + real(8) engfbp,virfbp,engsrp,virsrp,engcpe,vircpe,vircon,vircom + real(8) engfld,virfld,engshl,virshl,shlke,engtet,virtet,virpmf +- real(8) consv,engke,engrot,sigma,virtot,engcfg ++ real(8) consv,engke,engrot,sigma,virtot,engcfg,prntim,simtim + real(8) stpeng,stpeth,stpprs,stptmp,stpvir,stpvol,width,zlen + real(8) timelp,engmet,virmet,pass0,pass1,pass2,rlxtol,opttol + real(8) catchrad,sprneb,deltad,tlow,engtke,ehit,xhit,yhit,zhit +- real(8) ebias,vmin,boost,heinc,tboost,hyp_units,estar +- ++ real(8) ebias,vmin,hyp_units,estar,chit_shl,sigma_shl ++ real(8) engord,virord + real(8), allocatable :: tbuffer(:) + + data timelp/0.d0/,lminnow/.false./,ntrack/10/ +- data npage,lines/8,0/,recycle/.true./,boost/1.d0/ ++ data npage,lines/8,0/,recycle/.true./ + data pass0/0.d0/,pass1/0.d0/,pass2/0.d0/ + data delr,epsq,press,quattol,rprim,rvdw/6*0.d0/ + data temp,timcls,timjob,tolnce,rlxtol/5*0.d0/ +-CVAM +-CVAM include 'VT.inc' +-CVAM + + c set up the communications + + call initcomms() + call gsync() + +-c set up VAMPIR +- +-CVAM call VTSETUP() +-CVAM call VTTRACEON(ierr) +-CVAM call VTBEGIN(99, ierr) +- + c determine processor identities + + call machine(idnode,mxnode) +- +-c open main printing file +- +- if(idnode.eq.0)open(nrite,file='OUTPUT') +- if(idnode.eq.0) write (nrite, +- x "(/,20x,'DL_POLY Version 2.20', +- x /,/,30x,'Running on ',i4,' nodes',/,/)") mxnode +- ++ + c activate for limited-life executable + + CBOMB call bomb(idnode,2008,6,30) + + allocate (tbuffer(10),stat=memr) + +- call parset(idnode,mxnode,tbuffer) ++ call parset(redirect,idnode,mxnode,tbuffer) ++ ++c open main printing file + ++ if(.not.redirect.and.idnode.eq.0)open(nrite,file='OUTPUT') ++ if(idnode.eq.0) write (nrite, ++ x "(/,20x,'DL_POLY Classic 1.9', ++ x /,/,30x,'Running on ',i4,' nodes',/,/)") mxnode ++ + c allocate arrays for each function + + call alloc_ang_arrays(idnode) +@@ -184,24 +166,24 @@ + c input the control parameters defining the simulation + + call simdef +- x (lfcap,lgofr,lnsq,loptim,lzero,lminim,lpgr,ltraj,ltscal,lzeql, +- x lzden,nolink,newgau,lhit,lbpd,ltad,lneb,prechk,tadall,lsolva, +- x lfree,lfrmas,lexcite,lswitch,lghost,idnode,minstp,intsta,istraj, +- x keybpd,keyens,keyfce,keyres,keyver,keytrj,kmax1,kmax2,kmax3, +- x multt,nstack,nstbgr,nsbzdn,nstbpo,nhko,nlatt,nstbts,nsteql, +- x nstraj,nstrun,nospl,keytol,numgau,khit,nhit,nblock,ntrack, +- x blkout,numneb,mode,nsolva,isolva,alpha,delr,epsq,fmax,press, +- x quattol,rcut,rprim,rvdw,taup,taut,temp,timcls,timjob,tolnce, +- x tstep,rlxtol,opttol,zlen,ehit,xhit,yhit,zhit,ebias,vmin,heinc, +- x catchrad,sprneb,deltad,tlow,hyp_units) ++ x (seek,lfcap,lgofr,lnsq,loptim,lzero,lminim,lpgr,ltraj,ltscal, ++ x lzeql,lzden,nolink,newgau,lhit,lbpd,ltad,lneb,prechk,tadall, ++ x lsolva,lfree,lfrmas,lexcite,lswitch,lghost,lnfic,nebgo,lpsoc, ++ x idnode,minstp,intsta,istraj,keybpd,keyens,keyfce,keyres,keyver, ++ x keytrj,kmax1,kmax2,kmax3,multt,nstack,nstbgr,nsbzdn,nstbpo, ++ x nhko,nlatt,nstbts,nsteql,nstraj,nstrun,nospl,keytol,numgau, ++ x khit,nhit,nblock,ntrack,blkout,numneb,mode,nsolva,isolva,nofic, ++ x alpha,delr,epsq,fmax,press,quattol,rcut,rprim,rvdw,taup,taut, ++ x temp,timcls,timjob,tolnce,tstep,rlxtol,opttol,zlen,ehit,xhit, ++ x yhit,zhit,ebias,vmin,catchrad,sprneb,deltad,tlow,hyp_units) + + c input the system force field + + call sysdef + x (lneut,lnsq,lsolva,lfree,lexcite,lswitch,lghost,idnode,keyfce, + x keyfld,natms,ngrp,ntpatm,ntpmls,ntpvdw,ntptbp,ntpmet,ntpfbp, +- x ntpter,nshels,keyshl,ntghost,dlrpot,engunit,rvdw,rcuttb,rctter, +- x rcutfb) ++ x ntpter,nshels,keyshl,ntghost,keyver,dlrpot,engunit,rvdw,rcuttb, ++ x rctter,rcutfb) + + if(ntpmet.gt.0.and.multt.gt.1)call error(idnode,153) + +@@ -237,11 +219,23 @@ + c read thermodynamic and structural data from restart file + + call sysinit +- x (lgofr,lzden,lsolva,lfree,lghost,idnode,imcon,keyfce, ++ x (lgofr,lzden,lsolva,lfree,lghost,lpsoc,idnode,imcon,keyfce, + x keyres,mxnode,natms,ntshl,nstep,numacc,numrdf,ntpatm, + x ntpmet,ntpvdw,nzden,chip,chit,conint,elrc,engunit,virlrc, +- x rvdw,volm,virtot,vircom,tboost) ++ x rvdw,volm,virtot,vircom,tboost,chit_shl) + ++c metadynamics by d. quigley ++ ++ if(lmetadyn) then ++ ++c make copy of excluded atom list for use by metadynamics ++ call exclude_copy_mtd(idnode) ++ ++c initialise metadynamics, read order parameter definitions etc. ++ call define_metadynamics(idnode,mxnode,natms,ntpatm,temp) ++ ++ end if ++ + c synchronise LRC, SIC and system charge terms for switching + + llswitch=.false. +@@ -283,6 +277,19 @@ + + sigma=temp*boltz*degfre*0.5d0 + ++c metadynamics by d. quigley ++ ++ sigma_shl=boltz*degshl*0.5d0 ++ ++c convert BPD parameters to internal units ++ ++ if(lbpd)then ++ ++ ebias=0.5d0*boltz*degfre*ebias ++ vmin=0.5d0*boltz*degfre*vmin ++ ++ endif ++ + c time check + + call timchk(1,tzero) +@@ -309,7 +316,7 @@ + x rcut,rcutfb,rcuttb,rprim,rvdw,shlke,engcfg,temp,tstep, + x virang,virbnd,vircpe,virdih,virfbp,virfld,virinv,virlrc, + x virmet,virshl,virsrp,virtbp,virter,virtet,volm,engmet, +- x virtot,sigma,tolnce,engunit) ++ x virtot,sigma,tolnce,engunit,engord,virord) + + c calculate initial conditions for velocity verlet + +@@ -340,12 +347,11 @@ + x opttol,rctter,rcut,rcutfb,rcuttb,rprim,rvdw,shlke, + x engcfg,temp,tstep,virang,virbnd,vircpe,virdih, + x virfbp,virfld,virinv,virlrc,virmet,virshl,virsrp, +- x virtbp,virter,virtet,volm,engmet,virtot) ++ x virtbp,virter,virtet,volm,engmet,virtot,engord,virord) + + c bias potential dynamics option - reset forces + +- if(lbpd)call bpd_forces +- x (natms,vmin,ebias,temp,engcfg,boost) ++ if(lbpd)call bpd_forces(natms,keybpd,vmin,ebias,temp,engcfg) + + endif + +@@ -354,14 +360,14 @@ + c construct the first reference state + + call hyper_start +- x (lbpd,lfcap,lneut,lnsq,loglnk,lzeql,newlst,nblock,idnode, ++ x (ltad,lbpd,lfcap,lneut,lnsq,loglnk,lzeql,newlst,nblock,idnode, + x imcon,keyfce,keyfld,keyshl,keytol,kmax1,kmax2,kmax3,multt, + x mxnode,natms,ngrp,nhko,nlatt,nneut,nospl,nscons,nstbgr, + x nstep,nsteql,ntangl,ntbond,ntdihd,ntfree,ntinv,ntpfbp, +- x ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,ntcons,alpha, ++ x ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,ntcons,ntrack,alpha, + x delr,dlrpot,drewd,elrc,virlrc,epsq,fmax,opttol,rctter, + x rcut,rcutfb,rcuttb,rprim,rvdw,temp,tstep,volm,sigma, +- x tboost,hyp_units) ++ x hyp_units) + + endif + +@@ -430,7 +436,7 @@ + vxo_fre(:)=vxx(:) + vyo_fre(:)=vyy(:) + vzo_fre(:)=vzz(:) +- ++ + endif + + endif +@@ -524,10 +530,11 @@ + if(llswitch)call copy_force(idnode,mxnode) + + call vv_integrate +- x (lcnb,lshmov,isw,idnode,mxnode,imcon,natms2,ngrp,keyens, +- x nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,tstep,engke, +- x engrot,tolnce,vircon,vircom,virtot,temp,press,volm,sigma, +- x taut,taup,chit,chip,consv,conint,elrc,virlrc,virpmf) ++ x (lcnb,lshmov,lnfic,isw,idnode,mxnode,imcon,natms2,nstep, ++ x ngrp,keyens,nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode, ++ x nofic,ntshl,keyshl,tstep,engke,engrot,tolnce,vircon,vircom, ++ x virtot,temp,press,volm,sigma,taut,taup,chit,chip,consv, ++ x conint,elrc,virlrc,virpmf,chit_shl,sigma_shl) + + if(lghost)call update_ghost(idnode,mxnode) + +@@ -560,10 +567,10 @@ + x rcut,rcutfb,rcuttb,rprim,rvdw,shlke,engcfg,temp,tstep, + x virang,virbnd,vircpe,virdih,virfbp,virfld,virinv,virlrc, + x virmet,virshl,virsrp,virtbp,virter,virtet,volm,engmet, +- x virtot,sigma,tolnce,engunit) ++ x virtot,sigma,tolnce,engunit,engord,virord) + + elseif(loptim.or.keyshl.ne.2)then +- ++ + call molecular_dynamics + x (lfcap,lgofr,lneut,lnsq,loglnk,loptim,lzeql,lzero, + x newlst,stropt,recycle,ltad,lsolva,lfree,lghost, +@@ -577,7 +584,7 @@ + x opttol,rctter,rcut,rcutfb,rcuttb,rprim,rvdw,shlke, + x engcfg,temp,tstep,virang,virbnd,vircpe,virdih, + x virfbp,virfld,virinv,virlrc,virmet,virshl,virsrp, +- x virtbp,virter,virtet,volm,engmet,virtot) ++ x virtbp,virter,virtet,volm,engmet,virtot,engord,virord) + + else + +@@ -593,14 +600,13 @@ + x rprim,rvdw,shlke,engcfg,temp,tstep,virang,virbnd,vircpe, + x virdih,virfbp,virfld,virinv,virlrc,virmet,virshl,virsrp, + x virtbp,virter,virtet,volm,engmet,virtot,rlxtol,pass0, +- x pass1,pass2) ++ x pass1,pass2,engord,virord) + + endif + + c bias potential dynamics option - reset forces + +- if(lbpd)call bpd_forces +- x (natms,vmin,ebias,temp,engcfg,boost) ++ if(lbpd)call bpd_forces(natms,keybpd,vmin,ebias,temp,engcfg) + + c switching option for excitation simulation + +@@ -613,11 +619,11 @@ + c integrate equations of motion by leapfrog verlet + + if(.not.(loptim.or.lminnow))call lf_integrate +- x (lcnb,lshmov,idnode,mxnode,imcon,natms2,ngrp,keyens, +- x nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,tstep,engke, +- x engrot,tolnce,quattol,vircon,vircom,virtot,temp,press, +- x volm,sigma,taut,taup,chit,chip,consv,conint,elrc, +- x virlrc,virpmf) ++ x (lcnb,lshmov,lnfic,idnode,mxnode,imcon,natms2,nstep,ngrp, ++ x keyens,nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,nofic, ++ x tstep,engke,engrot,tolnce,quattol,vircon,vircom,virtot, ++ x temp,press,volm,sigma,taut,taup,chit,chip,consv,conint, ++ x elrc,virlrc,virpmf) + + else if(keyver.gt.0)then + +@@ -625,11 +631,11 @@ + + isw=2 + if(.not.loptim)call vv_integrate +- x (lcnb,lshmov,isw,idnode,mxnode,imcon,natms2,ngrp,keyens, +- x nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,tstep,engke, +- x engrot,tolnce,vircon,vircom,virtot,temp,press, +- x volm,sigma,taut,taup,chit,chip,consv,conint,elrc, +- x virlrc,virpmf) ++ x (lcnb,lshmov,lnfic,isw,idnode,mxnode,imcon,natms2,nstep, ++ x ngrp,keyens,nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode, ++ x nofic,ntshl,keyshl,tstep,engke,engrot,tolnce,vircon,vircom, ++ x virtot,temp,press,volm,sigma,taut,taup,chit,chip,consv, ++ x conint,elrc,virlrc,virpmf,chit_shl,sigma_shl) + + endif + +@@ -651,23 +657,36 @@ + + engtke=engke+engrot + call hyper_driver +- x (ltad,lbpd,recycle,lfcap,lneut,lnsq,loglnk,lzeql,newlst, +- x prechk,tadall,nblock,ntrack,idnode,imcon,keyfce,keyfld, +- x keyshl,keytol,kmax1,kmax2,kmax3,multt,mxnode,natms,ngrp, +- x ntcons,nhko,nlatt,nneut,nospl,nscons,nstbgr,nstep, +- x nsteql,ntangl,ntbond,ntdihd,ntfree,ntinv,ntpfbp, +- x ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,blkout, ++ x (seek,ltad,lbpd,recycle,lfcap,lneut,lnsq,loglnk,lzeql, ++ x newlst,prechk,tadall,nebgo,nblock,ntrack,idnode,imcon, ++ x keyfce,keyfld,keyshl,keytol,kmax1,kmax2,kmax3,multt, ++ x mxnode,natms,ngrp,ntcons,nhko,nlatt,nneut,nospl,nscons, ++ x nstbgr,nstep,nsteql,ntangl,ntbond,ntdihd,ntfree,ntinv, ++ x ntpfbp,ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,blkout, + x alpha,delr,dlrpot,drewd,elrc,virlrc,epsq,fmax, + x opttol,rctter,rcut,rcutfb,rcuttb,rprim,rvdw,temp, + x tstep,volm,engcfg,catchrad,sprneb,deltad,tlow,engtke, +- x tolnce,tboost,hyp_units) ++ x tolnce,hyp_units,ebias,vmin) ++ ++ endif ++ ++c reset average boost factor in BPD during equilibration ++ ++ if(lbpd.and.keybpd.eq.1)then ++ ++ if(lzeql.and.nstep.le.nsteql)then ++ ++ numbpd=0 ++ tboost=0.d0 + + endif + ++ endif ++ + c calculate shell kinetic energy + + if(keyshl.eq.1)then +- ++ + call corshl(idnode,mxnode,ntshl,shlke) + + endif +@@ -686,6 +705,7 @@ + x mod(nstep-nsteql,nstbts).eq.0)then + + chit=0.d0 ++ chit_shl=0.d0 + chip=0.d0 + do i=1,9 + eta(i)=0.d0 +@@ -722,13 +742,13 @@ + + if(nstep.gt.0)call static + x (lbpd,lzeql,idnode,intsta,imcon,keyens,natms,nstack, +- x nstep,nsteql,ntpatm,numacc,mxnode,nblock,consv,degfre, +- x degrot,engang,engbnd,engcpe,engdih,enginv,engke,engrot, +- x engsrp,engunit,engcfg,stpeng,stpeth,stpprs,stptmp,stpvir, +- x stpvol,tstep,virbnd,engfbp,vircom,vircon,vircpe,virsrp, +- x engfld,virfld,engtbp,virtbp,virpmf,virshl,engshl,engtet, +- x virtet,degshl,shlke,virang,width,engmet,virmet,engter, +- x virter,boost,tboost,ebias,heinc) ++ x nstep,nsteql,ntpatm,numacc,mxnode,nblock,keybpd,numbpd, ++ x consv,degfre,degrot,engang,engbnd,engcpe,engdih,enginv, ++ x engke,engrot,engsrp,engunit,engcfg,stpeng,stpeth,stpprs, ++ x stptmp,stpvir,stpvol,tstep,virbnd,engfbp,vircom,vircon, ++ x vircpe,virsrp,engfld,virfld,engtbp,virtbp,virpmf,virshl, ++ x engshl,engtet,virtet,degshl,shlke,virang,width,engmet, ++ x virmet,engter,virter,boost,tboost) + + c z density calculation + +@@ -746,41 +766,39 @@ + call revive + x (lgofr,lzden,idnode,imcon,mxnode,natms,levcfg,nstep,nzden, + x numacc,numrdf,chip,chit,conint,tstep,engcfg,virtot,vircom, +- x tboost) ++ x tboost,chit_shl) + call error(idnode,95) + + endif + + c line-printer output every nstbpo steps + +-CVAM +-CVAM call VTBEGIN(68, ierr) +-CVAM +- + if(nstep.eq.1.or.(nstep.gt.1.and.mod(nstep,nstbpo).eq.0))then +- ++ + call timchk(0,timelp) + if(idnode.eq.0)then + ++ call get_prntime(hms,timelp,prntim) ++ call get_simtime(dec,nstep,tstep,simtim) + if(mod(lines,npage).eq.0) + x write(nrite,"(1x,120('-'), + x /,/,1x,' step',5x,'eng_tot',4x,'temp_tot',5x, + x 'eng_cfg',5x,'eng_vdw',5x,'eng_cou',5x,'eng_bnd', + x 5x,'eng_ang',5x,'eng_dih',5x,'eng_tet',/,1x, +- x 'time(ps)',5x,' eng_pv',4x,'temp_rot',5x,'vir_cfg', ++ x 'time ',5x,' eng_pv',4x,'temp_rot',5x,'vir_cfg', + x 5x,'vir_vdw',5x,'vir_cou',5x,'vir_bnd',5x,'vir_ang', +- x 5x,'vir_con',5x,'vir_tet',/,1x,'cpu (s)',6x, ++ x 5x,'vir_con',5x,'vir_tet',/,1x,'cpu time',6x, + x 'volume',4x,'temp_shl',5x,'eng_shl',5x,'vir_shl', + x 7x,'alpha',8x,'beta',7x,'gamma',5x,'vir_pmf', + x 7x,'press',/,/, +- x 1x,120('-'))") +- write(nrite,"(1x,i8,1p,9e12.4,/,1x,0p,f8.1,1p,9e12.4, +- x /,1x,0p,f8.1,1p,9e12.4)") ++ x 1x,120('-'))") ++ write(nrite,"(1x,i8,1p,9e12.4,/,1x,0p,f7.3,a1,1p,9e12.4, ++ x /,1x,0p,f7.3,a1,1p,9e12.4)") + x nstep,(stpval(i),i=1,9), +- x dble(nstep)*tstep,(stpval(i),i=10,18), +- x timelp,(stpval(i),i=19,27) ++ x simtim,dec,(stpval(i),i=10,18), ++ x prntim,hms,(stpval(i),i=19,27) + write(nrite,"(/,1x,' rolling',1p,9e12.4,/,1x,'averages', +- x 1p,9e12.4,/,9x,9e12.4)") (ravval(i),i=1,27) ++ x 1p,9e12.4,/,9x,1p,9e12.4)") (ravval(i),i=1,27) + write(nrite,"(1x,120('-'))") + + endif +@@ -788,9 +806,7 @@ + lines=lines+1 + + endif +-CVAM +-CVAM call VTEND(68, ierr) +-CVAM ++ + c report end of equilibration period + + if((.not.loptim).and.(.not.lzero).and.(nstep.ge.nsteql))then +@@ -850,9 +866,10 @@ + call revive + x (lgofr,lzden,idnode,imcon,mxnode,natms,levcfg,nstep,nzden, + x numacc,numrdf,chip,chit,conint,tstep,engcfg,virtot,vircom, +- x tboost) ++ x tboost,chit_shl) + +- if(ltad.or.lbpd)call hyper_close(idnode,mxnode,natms,nsteql) ++ if(ltad.or.lbpd) ++ x call hyper_close(ltad,idnode,mxnode,natms,nsteql) + + endif + +@@ -870,11 +887,11 @@ + c last time check + + call timchk(0,timelp) +- ++ call get_prntime(hms,timjob,prntim) + if(idnode.eq.0)write(nrite, +- x "(/,/,1x,'run terminating. elapsed cpu time = ',f13.3, +- x ', job time = ',f13.3,', close time = ',f13.3,/)") +- x timelp,timjob,timcls ++ x "(/,/,1x,'run terminating. elapsed cpu time = ',1p,e13.5, ++ x ', job time = ',0p,f7.3,a1,', close time = ',f7.2,'s',/)") ++ x timelp,prntim,hms,timcls + + c shell relaxation convergence statistics + +@@ -891,13 +908,15 @@ + levcfg=2 + if(loptim)levcfg=0 + if(.not.lneb)call result +- x (lbpd,lgofr,lpgr,lzden,idnode,imcon,keyens,mxnode,natms, +- x levcfg,nzden,nstep,ntpatm,numacc,numrdf,chip,chit,conint, +- x rcut,tstep,engcfg,volm,virtot,vircom,zlen,tboost) ++ x (ltad,lbpd,lgofr,lpgr,lzden,idnode,imcon,keyens,mxnode,natms, ++ x levcfg,nzden,nstep,ntpatm,numacc,numrdf,keybpd,chip,chit, ++ x conint,rcut,tstep,engcfg,volm,virtot,vircom,zlen,tboost, ++ x chit_shl) + + c write hyperdynamics restart file + +- if(ltad.or.lbpd)call hyper_close(idnode,mxnode,natms,nsteql) ++ if(ltad.or.lbpd) ++ x call hyper_close(ltad,idnode,mxnode,natms,nsteql) + + c close output channels + +@@ -911,9 +930,7 @@ + endif + + c terminate job +-CVAM +-CVAM call VTEND(99, ierr) +-CVAM ++ + call exitcomms() + + end +--- dlpoly-2.20.diff/srcmod/dlpoly.f.orig 2015-09-15 11:23:19.383901148 +0200 ++++ dlpoly-2.20.diff/srcmod/dlpoly.f 2016-11-25 18:01:54.766283535 +0100 +@@ -1,21 +1,14 @@ +- program dlpoly ++ program dlpoly_classic + + c*********************************************************************** + c +-c dl_poly is an cclrc/ccp5 program package for the dynamical +-c simulation of molecular systems. ++c dl_poly classic is an stfc/ccp5 program package for the ++c dynamical simulation of molecular systems. + c +-c dl_poly is the property of the cclrc daresbury laboratory, +-c daresbury, warrington wa4 4ad. no part of the package may +-c be redistributed to third parties without the consent of +-c daresbury laboratory. ++c dl_poly is the copyright of the stfc daresbury laboratory, ++c daresbury, warrington wa4 4ad. + c +-c dl_poly is available free of charge to academic institutions +-c engaged in non-commercial research only. potential users not +-c in this category must consult the ccp5 program librarian at +-c daresbury to negotiate terms of use. +-c +-c neither the cclrc, daresbury laboratory, ccp5 nor the authors ++c neither the stfc, daresbury laboratory, ccp5 nor the authors + c of this package claim that it is free from errors and do not + c accept liability for any loss or damage that may arise from + c its use. it is the users responsibility to verify that the +@@ -23,19 +16,13 @@ + c it. + c + c users of this package are recommended to consult the dl_poly +-c user and reference manuals for the full terms and conditions +-c of its use. ++c user manual for the full description of its use and purpose. + c + c authors: w.smith and t.r.forester 1995 + c copyright daresbury laboratory 1995 + c +-c release 2.20 +-c +-c wl +-c 2009/01/15 11:55:48 +-c 1.20 +-c Exp +-c ++c DL_POLY CLASSIC VERSION 1.9 ++c + c*********************************************************************** + + c declare required modules +@@ -57,6 +44,7 @@ + use integrator_module + use inversion_module + use metal_module ++ use metafreeze_module + use nlist_builders_module + use pair_module + use pmf_module +@@ -76,11 +64,14 @@ + + implicit none + ++ character*1 hms,dec ++ character*8 seek ++ + logical ltscal,lzeql,loptim,ltraj,lgofr,lpgr,lfcap,recycle + logical newlst,lneut,loglnk,lnsq,lzden,lshmov,lcnb,ltad,lneb + logical stropt,lzero,nolink,newgau,lminim,lminnow,lhit,lbpd + logical prechk,tadall,lexcite,lsolva,lfree,lfrmas,lswitch +- logical lghost,llswitch ++ logical lghost,llswitch,lnfic,nebgo,lpsoc,redirect + + integer npage,lines,idnode,mxnode,memr,intsta,istraj,nsbzdn + integer keyens,keyfce,keyres,keytrj,kmax1,kmax2,kmax3,multt +@@ -91,7 +82,7 @@ + integer ntteth,ntshl,nstep,numacc,numrdf,nzden,nscons,i,k + integer ntpter,keyshl,isw,keyver,keystr,keytol,numgau,khit + integer nhit,keybpd,ntrack,nblock,blkout,numneb,nturn,mode +- integer natms2,ntghost,nsolva,isolva ++ integer natms2,ntghost,nsolva,isolva,nofic + + real(8) alpha,delr,epsq,fmax,press,quattol,rcut,rprim,rvdw,taup + real(8) taut,temp,timcls,timjob,tolnce,tstep,tzero,dlrpot,drewd +@@ -100,58 +91,50 @@ + real(8) engdih,virdih,enginv,virinv,engtbp,virtbp,engter,virter + real(8) engfbp,virfbp,engsrp,virsrp,engcpe,vircpe,vircon,vircom + real(8) engfld,virfld,engshl,virshl,shlke,engtet,virtet,virpmf +- real(8) consv,engke,engrot,sigma,virtot,engcfg ++ real(8) consv,engke,engrot,sigma,virtot,engcfg,prntim,simtim + real(8) stpeng,stpeth,stpprs,stptmp,stpvir,stpvol,width,zlen + real(8) timelp,engmet,virmet,pass0,pass1,pass2,rlxtol,opttol + real(8) catchrad,sprneb,deltad,tlow,engtke,ehit,xhit,yhit,zhit +- real(8) ebias,vmin,boost,heinc,tboost,hyp_units,estar ++ real(8) ebias,vmin,hyp_units,estar,chit_shl,sigma_shl ++ real(8) engord,virord + c PLUMED modifications + real(8) energyUnits,lengthUnits,timeUnits + integer(8) get_comms + c PLUMED modifications +- ++ + real(8), allocatable :: tbuffer(:) + integer :: plumedavaiable + + data timelp/0.d0/,lminnow/.false./,ntrack/10/ +- data npage,lines/8,0/,recycle/.true./,boost/1.d0/ ++ data npage,lines/8,0/,recycle/.true./ + data pass0/0.d0/,pass1/0.d0/,pass2/0.d0/ + data delr,epsq,press,quattol,rprim,rvdw/6*0.d0/ + data temp,timcls,timjob,tolnce,rlxtol/5*0.d0/ +-CVAM +-CVAM include 'VT.inc' +-CVAM + + c set up the communications + + call initcomms() + call gsync() + +-c set up VAMPIR +- +-CVAM call VTSETUP() +-CVAM call VTTRACEON(ierr) +-CVAM call VTBEGIN(99, ierr) +- + c determine processor identities + + call machine(idnode,mxnode) +- +-c open main printing file +- +- if(idnode.eq.0)open(nrite,file='OUTPUT') +- if(idnode.eq.0) write (nrite, +- x "(/,20x,'DL_POLY Version 2.20', +- x /,/,30x,'Running on ',i4,' nodes',/,/)") mxnode +- ++ + c activate for limited-life executable + + CBOMB call bomb(idnode,2008,6,30) + + allocate (tbuffer(10),stat=memr) + +- call parset(idnode,mxnode,tbuffer) ++ call parset(redirect,idnode,mxnode,tbuffer) ++ ++c open main printing file + ++ if(.not.redirect.and.idnode.eq.0)open(nrite,file='OUTPUT') ++ if(idnode.eq.0) write (nrite, ++ x "(/,20x,'DL_POLY Classic 1.9', ++ x /,/,30x,'Running on ',i4,' nodes',/,/)") mxnode ++ + c allocate arrays for each function + + call alloc_ang_arrays(idnode) +@@ -189,24 +172,24 @@ + c input the control parameters defining the simulation + + call simdef +- x (lfcap,lgofr,lnsq,loptim,lzero,lminim,lpgr,ltraj,ltscal,lzeql, +- x lzden,nolink,newgau,lhit,lbpd,ltad,lneb,prechk,tadall,lsolva, +- x lfree,lfrmas,lexcite,lswitch,lghost,idnode,minstp,intsta,istraj, +- x keybpd,keyens,keyfce,keyres,keyver,keytrj,kmax1,kmax2,kmax3, +- x multt,nstack,nstbgr,nsbzdn,nstbpo,nhko,nlatt,nstbts,nsteql, +- x nstraj,nstrun,nospl,keytol,numgau,khit,nhit,nblock,ntrack, +- x blkout,numneb,mode,nsolva,isolva,alpha,delr,epsq,fmax,press, +- x quattol,rcut,rprim,rvdw,taup,taut,temp,timcls,timjob,tolnce, +- x tstep,rlxtol,opttol,zlen,ehit,xhit,yhit,zhit,ebias,vmin,heinc, +- x catchrad,sprneb,deltad,tlow,hyp_units) ++ x (seek,lfcap,lgofr,lnsq,loptim,lzero,lminim,lpgr,ltraj,ltscal, ++ x lzeql,lzden,nolink,newgau,lhit,lbpd,ltad,lneb,prechk,tadall, ++ x lsolva,lfree,lfrmas,lexcite,lswitch,lghost,lnfic,nebgo,lpsoc, ++ x idnode,minstp,intsta,istraj,keybpd,keyens,keyfce,keyres,keyver, ++ x keytrj,kmax1,kmax2,kmax3,multt,nstack,nstbgr,nsbzdn,nstbpo, ++ x nhko,nlatt,nstbts,nsteql,nstraj,nstrun,nospl,keytol,numgau, ++ x khit,nhit,nblock,ntrack,blkout,numneb,mode,nsolva,isolva,nofic, ++ x alpha,delr,epsq,fmax,press,quattol,rcut,rprim,rvdw,taup,taut, ++ x temp,timcls,timjob,tolnce,tstep,rlxtol,opttol,zlen,ehit,xhit, ++ x yhit,zhit,ebias,vmin,catchrad,sprneb,deltad,tlow,hyp_units) + + c input the system force field + + call sysdef + x (lneut,lnsq,lsolva,lfree,lexcite,lswitch,lghost,idnode,keyfce, + x keyfld,natms,ngrp,ntpatm,ntpmls,ntpvdw,ntptbp,ntpmet,ntpfbp, +- x ntpter,nshels,keyshl,ntghost,dlrpot,engunit,rvdw,rcuttb,rctter, +- x rcutfb) ++ x ntpter,nshels,keyshl,ntghost,keyver,dlrpot,engunit,rvdw,rcuttb, ++ x rctter,rcutfb) + + if(ntpmet.gt.0.and.multt.gt.1)call error(idnode,153) + +@@ -242,11 +225,23 @@ + c read thermodynamic and structural data from restart file + + call sysinit +- x (lgofr,lzden,lsolva,lfree,lghost,idnode,imcon,keyfce, ++ x (lgofr,lzden,lsolva,lfree,lghost,lpsoc,idnode,imcon,keyfce, + x keyres,mxnode,natms,ntshl,nstep,numacc,numrdf,ntpatm, + x ntpmet,ntpvdw,nzden,chip,chit,conint,elrc,engunit,virlrc, +- x rvdw,volm,virtot,vircom,tboost) ++ x rvdw,volm,virtot,vircom,tboost,chit_shl) + ++c metadynamics by d. quigley ++ ++ if(lmetadyn) then ++ ++c make copy of excluded atom list for use by metadynamics ++ call exclude_copy_mtd(idnode) ++ ++c initialise metadynamics, read order parameter definitions etc. ++ call define_metadynamics(idnode,mxnode,natms,ntpatm,temp) ++ ++ end if ++ + c synchronise LRC, SIC and system charge terms for switching + + llswitch=.false. +@@ -317,6 +312,19 @@ + + sigma=temp*boltz*degfre*0.5d0 + ++c metadynamics by d. quigley ++ ++ sigma_shl=boltz*degshl*0.5d0 ++ ++c convert BPD parameters to internal units ++ ++ if(lbpd)then ++ ++ ebias=0.5d0*boltz*degfre*ebias ++ vmin=0.5d0*boltz*degfre*vmin ++ ++ endif ++ + c time check + + call timchk(1,tzero) +@@ -343,7 +351,7 @@ + x rcut,rcutfb,rcuttb,rprim,rvdw,shlke,engcfg,temp,tstep, + x virang,virbnd,vircpe,virdih,virfbp,virfld,virinv,virlrc, + x virmet,virshl,virsrp,virtbp,virter,virtet,volm,engmet, +- x virtot,sigma,tolnce,engunit) ++ x virtot,sigma,tolnce,engunit,engord,virord) + + c calculate initial conditions for velocity verlet + +@@ -374,12 +382,11 @@ + x opttol,rctter,rcut,rcutfb,rcuttb,rprim,rvdw,shlke, + x engcfg,temp,tstep,virang,virbnd,vircpe,virdih, + x virfbp,virfld,virinv,virlrc,virmet,virshl,virsrp, +- x virtbp,virter,virtet,volm,engmet,virtot) ++ x virtbp,virter,virtet,volm,engmet,virtot,engord,virord) + + c bias potential dynamics option - reset forces + +- if(lbpd)call bpd_forces +- x (natms,vmin,ebias,temp,engcfg,boost) ++ if(lbpd)call bpd_forces(natms,keybpd,vmin,ebias,temp,engcfg) + + endif + +@@ -388,14 +395,14 @@ + c construct the first reference state + + call hyper_start +- x (lbpd,lfcap,lneut,lnsq,loglnk,lzeql,newlst,nblock,idnode, ++ x (ltad,lbpd,lfcap,lneut,lnsq,loglnk,lzeql,newlst,nblock,idnode, + x imcon,keyfce,keyfld,keyshl,keytol,kmax1,kmax2,kmax3,multt, + x mxnode,natms,ngrp,nhko,nlatt,nneut,nospl,nscons,nstbgr, + x nstep,nsteql,ntangl,ntbond,ntdihd,ntfree,ntinv,ntpfbp, +- x ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,ntcons,alpha, ++ x ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,ntcons,ntrack,alpha, + x delr,dlrpot,drewd,elrc,virlrc,epsq,fmax,opttol,rctter, + x rcut,rcutfb,rcuttb,rprim,rvdw,temp,tstep,volm,sigma, +- x tboost,hyp_units) ++ x hyp_units) + + endif + +@@ -464,7 +471,7 @@ + vxo_fre(:)=vxx(:) + vyo_fre(:)=vyy(:) + vzo_fre(:)=vzz(:) +- ++ + endif + + endif +@@ -558,10 +565,11 @@ + if(llswitch)call copy_force(idnode,mxnode) + + call vv_integrate +- x (lcnb,lshmov,isw,idnode,mxnode,imcon,natms2,ngrp,keyens, +- x nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,tstep,engke, +- x engrot,tolnce,vircon,vircom,virtot,temp,press,volm,sigma, +- x taut,taup,chit,chip,consv,conint,elrc,virlrc,virpmf) ++ x (lcnb,lshmov,lnfic,isw,idnode,mxnode,imcon,natms2,nstep, ++ x ngrp,keyens,nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode, ++ x nofic,ntshl,keyshl,tstep,engke,engrot,tolnce,vircon,vircom, ++ x virtot,temp,press,volm,sigma,taut,taup,chit,chip,consv, ++ x conint,elrc,virlrc,virpmf,chit_shl,sigma_shl) + + if(lghost)call update_ghost(idnode,mxnode) + +@@ -594,10 +602,10 @@ + x rcut,rcutfb,rcuttb,rprim,rvdw,shlke,engcfg,temp,tstep, + x virang,virbnd,vircpe,virdih,virfbp,virfld,virinv,virlrc, + x virmet,virshl,virsrp,virtbp,virter,virtet,volm,engmet, +- x virtot,sigma,tolnce,engunit) ++ x virtot,sigma,tolnce,engunit,engord,virord) + + elseif(loptim.or.keyshl.ne.2)then +- ++ + call molecular_dynamics + x (lfcap,lgofr,lneut,lnsq,loglnk,loptim,lzeql,lzero, + x newlst,stropt,recycle,ltad,lsolva,lfree,lghost, +@@ -611,7 +619,7 @@ + x opttol,rctter,rcut,rcutfb,rcuttb,rprim,rvdw,shlke, + x engcfg,temp,tstep,virang,virbnd,vircpe,virdih, + x virfbp,virfld,virinv,virlrc,virmet,virshl,virsrp, +- x virtbp,virter,virtet,volm,engmet,virtot) ++ x virtbp,virter,virtet,volm,engmet,virtot,engord,virord) + + else + +@@ -627,14 +635,13 @@ + x rprim,rvdw,shlke,engcfg,temp,tstep,virang,virbnd,vircpe, + x virdih,virfbp,virfld,virinv,virlrc,virmet,virshl,virsrp, + x virtbp,virter,virtet,volm,engmet,virtot,rlxtol,pass0, +- x pass1,pass2) ++ x pass1,pass2,engord,virord) + + endif + + c bias potential dynamics option - reset forces + +- if(lbpd)call bpd_forces +- x (natms,vmin,ebias,temp,engcfg,boost) ++ if(lbpd)call bpd_forces(natms,keybpd,vmin,ebias,temp,engcfg) + + c switching option for excitation simulation + +@@ -647,11 +654,11 @@ + c integrate equations of motion by leapfrog verlet + + if(.not.(loptim.or.lminnow))call lf_integrate +- x (lcnb,lshmov,idnode,mxnode,imcon,natms2,ngrp,keyens, +- x nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,tstep,engke, +- x engrot,tolnce,quattol,vircon,vircom,virtot,temp,press, +- x volm,sigma,taut,taup,chit,chip,consv,conint,elrc, +- x virlrc,virpmf) ++ x (lcnb,lshmov,lnfic,idnode,mxnode,imcon,natms2,nstep,ngrp, ++ x keyens,nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,nofic, ++ x tstep,engke,engrot,tolnce,quattol,vircon,vircom,virtot, ++ x temp,press,volm,sigma,taut,taup,chit,chip,consv,conint, ++ x elrc,virlrc,virpmf) + + else if(keyver.gt.0)then + +@@ -659,11 +666,11 @@ + + isw=2 + if(.not.loptim)call vv_integrate +- x (lcnb,lshmov,isw,idnode,mxnode,imcon,natms2,ngrp,keyens, +- x nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode,tstep,engke, +- x engrot,tolnce,vircon,vircom,virtot,temp,press, +- x volm,sigma,taut,taup,chit,chip,consv,conint,elrc, +- x virlrc,virpmf) ++ x (lcnb,lshmov,lnfic,isw,idnode,mxnode,imcon,natms2,nstep, ++ x ngrp,keyens,nscons,ntcons,ntpatm,ntfree,nspmf,ntpmf,mode, ++ x nofic,ntshl,keyshl,tstep,engke,engrot,tolnce,vircon,vircom, ++ x virtot,temp,press,volm,sigma,taut,taup,chit,chip,consv, ++ x conint,elrc,virlrc,virpmf,chit_shl,sigma_shl) + + endif + +@@ -685,23 +692,36 @@ + + engtke=engke+engrot + call hyper_driver +- x (ltad,lbpd,recycle,lfcap,lneut,lnsq,loglnk,lzeql,newlst, +- x prechk,tadall,nblock,ntrack,idnode,imcon,keyfce,keyfld, +- x keyshl,keytol,kmax1,kmax2,kmax3,multt,mxnode,natms,ngrp, +- x ntcons,nhko,nlatt,nneut,nospl,nscons,nstbgr,nstep, +- x nsteql,ntangl,ntbond,ntdihd,ntfree,ntinv,ntpfbp, +- x ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,blkout, ++ x (seek,ltad,lbpd,recycle,lfcap,lneut,lnsq,loglnk,lzeql, ++ x newlst,prechk,tadall,nebgo,nblock,ntrack,idnode,imcon, ++ x keyfce,keyfld,keyshl,keytol,kmax1,kmax2,kmax3,multt, ++ x mxnode,natms,ngrp,ntcons,nhko,nlatt,nneut,nospl,nscons, ++ x nstbgr,nstep,nsteql,ntangl,ntbond,ntdihd,ntfree,ntinv, ++ x ntpfbp,ntpmet,ntptbp,ntpter,ntpvdw,ntshl,ntteth,blkout, + x alpha,delr,dlrpot,drewd,elrc,virlrc,epsq,fmax, + x opttol,rctter,rcut,rcutfb,rcuttb,rprim,rvdw,temp, + x tstep,volm,engcfg,catchrad,sprneb,deltad,tlow,engtke, +- x tolnce,tboost,hyp_units) ++ x tolnce,hyp_units,ebias,vmin) + + endif + ++c reset average boost factor in BPD during equilibration ++ ++ if(lbpd.and.keybpd.eq.1)then ++ ++ if(lzeql.and.nstep.le.nsteql)then ++ ++ numbpd=0 ++ tboost=0.d0 ++ ++ endif ++ ++ endif ++ + c calculate shell kinetic energy + + if(keyshl.eq.1)then +- ++ + call corshl(idnode,mxnode,ntshl,shlke) + + endif +@@ -720,6 +740,7 @@ + x mod(nstep-nsteql,nstbts).eq.0)then + + chit=0.d0 ++ chit_shl=0.d0 + chip=0.d0 + do i=1,9 + eta(i)=0.d0 +@@ -756,13 +777,13 @@ + + if(nstep.gt.0)call static + x (lbpd,lzeql,idnode,intsta,imcon,keyens,natms,nstack, +- x nstep,nsteql,ntpatm,numacc,mxnode,nblock,consv,degfre, +- x degrot,engang,engbnd,engcpe,engdih,enginv,engke,engrot, +- x engsrp,engunit,engcfg,stpeng,stpeth,stpprs,stptmp,stpvir, +- x stpvol,tstep,virbnd,engfbp,vircom,vircon,vircpe,virsrp, +- x engfld,virfld,engtbp,virtbp,virpmf,virshl,engshl,engtet, +- x virtet,degshl,shlke,virang,width,engmet,virmet,engter, +- x virter,boost,tboost,ebias,heinc) ++ x nstep,nsteql,ntpatm,numacc,mxnode,nblock,keybpd,numbpd, ++ x consv,degfre,degrot,engang,engbnd,engcpe,engdih,enginv, ++ x engke,engrot,engsrp,engunit,engcfg,stpeng,stpeth,stpprs, ++ x stptmp,stpvir,stpvol,tstep,virbnd,engfbp,vircom,vircon, ++ x vircpe,virsrp,engfld,virfld,engtbp,virtbp,virpmf,virshl, ++ x engshl,engtet,virtet,degshl,shlke,virang,width,engmet, ++ x virmet,engter,virter,boost,tboost) + + c z density calculation + +@@ -780,41 +801,39 @@ + call revive + x (lgofr,lzden,idnode,imcon,mxnode,natms,levcfg,nstep,nzden, + x numacc,numrdf,chip,chit,conint,tstep,engcfg,virtot,vircom, +- x tboost) ++ x tboost,chit_shl) + call error(idnode,95) + + endif + + c line-printer output every nstbpo steps + +-CVAM +-CVAM call VTBEGIN(68, ierr) +-CVAM +- + if(nstep.eq.1.or.(nstep.gt.1.and.mod(nstep,nstbpo).eq.0))then +- ++ + call timchk(0,timelp) + if(idnode.eq.0)then + ++ call get_prntime(hms,timelp,prntim) ++ call get_simtime(dec,nstep,tstep,simtim) + if(mod(lines,npage).eq.0) + x write(nrite,"(1x,120('-'), + x /,/,1x,' step',5x,'eng_tot',4x,'temp_tot',5x, + x 'eng_cfg',5x,'eng_vdw',5x,'eng_cou',5x,'eng_bnd', + x 5x,'eng_ang',5x,'eng_dih',5x,'eng_tet',/,1x, +- x 'time(ps)',5x,' eng_pv',4x,'temp_rot',5x,'vir_cfg', ++ x 'time ',5x,' eng_pv',4x,'temp_rot',5x,'vir_cfg', + x 5x,'vir_vdw',5x,'vir_cou',5x,'vir_bnd',5x,'vir_ang', +- x 5x,'vir_con',5x,'vir_tet',/,1x,'cpu (s)',6x, ++ x 5x,'vir_con',5x,'vir_tet',/,1x,'cpu time',6x, + x 'volume',4x,'temp_shl',5x,'eng_shl',5x,'vir_shl', + x 7x,'alpha',8x,'beta',7x,'gamma',5x,'vir_pmf', + x 7x,'press',/,/, +- x 1x,120('-'))") +- write(nrite,"(1x,i8,1p,9e12.4,/,1x,0p,f8.1,1p,9e12.4, +- x /,1x,0p,f8.1,1p,9e12.4)") ++ x 1x,120('-'))") ++ write(nrite,"(1x,i8,1p,9e12.4,/,1x,0p,f7.3,a1,1p,9e12.4, ++ x /,1x,0p,f7.3,a1,1p,9e12.4)") + x nstep,(stpval(i),i=1,9), +- x dble(nstep)*tstep,(stpval(i),i=10,18), +- x timelp,(stpval(i),i=19,27) ++ x simtim,dec,(stpval(i),i=10,18), ++ x prntim,hms,(stpval(i),i=19,27) + write(nrite,"(/,1x,' rolling',1p,9e12.4,/,1x,'averages', +- x 1p,9e12.4,/,9x,9e12.4)") (ravval(i),i=1,27) ++ x 1p,9e12.4,/,9x,1p,9e12.4)") (ravval(i),i=1,27) + write(nrite,"(1x,120('-'))") + + endif +@@ -822,9 +841,7 @@ + lines=lines+1 + + endif +-CVAM +-CVAM call VTEND(68, ierr) +-CVAM ++ + c report end of equilibration period + + if((.not.loptim).and.(.not.lzero).and.(nstep.ge.nsteql))then +@@ -884,9 +901,10 @@ + call revive + x (lgofr,lzden,idnode,imcon,mxnode,natms,levcfg,nstep,nzden, + x numacc,numrdf,chip,chit,conint,tstep,engcfg,virtot,vircom, +- x tboost) ++ x tboost,chit_shl) + +- if(ltad.or.lbpd)call hyper_close(idnode,mxnode,natms,nsteql) ++ if(ltad.or.lbpd) ++ x call hyper_close(ltad,idnode,mxnode,natms,nsteql) + + endif + +@@ -904,11 +922,11 @@ + c last time check + + call timchk(0,timelp) +- ++ call get_prntime(hms,timjob,prntim) + if(idnode.eq.0)write(nrite, +- x "(/,/,1x,'run terminating. elapsed cpu time = ',f13.3, +- x ', job time = ',f13.3,', close time = ',f13.3,/)") +- x timelp,timjob,timcls ++ x "(/,/,1x,'run terminating. elapsed cpu time = ',1p,e13.5, ++ x ', job time = ',0p,f7.3,a1,', close time = ',f7.2,'s',/)") ++ x timelp,prntim,hms,timcls + + c shell relaxation convergence statistics + +@@ -925,13 +943,15 @@ + levcfg=2 + if(loptim)levcfg=0 + if(.not.lneb)call result +- x (lbpd,lgofr,lpgr,lzden,idnode,imcon,keyens,mxnode,natms, +- x levcfg,nzden,nstep,ntpatm,numacc,numrdf,chip,chit,conint, +- x rcut,tstep,engcfg,volm,virtot,vircom,zlen,tboost) ++ x (ltad,lbpd,lgofr,lpgr,lzden,idnode,imcon,keyens,mxnode,natms, ++ x levcfg,nzden,nstep,ntpatm,numacc,numrdf,keybpd,chip,chit, ++ x conint,rcut,tstep,engcfg,volm,virtot,vircom,zlen,tboost, ++ x chit_shl) + + c write hyperdynamics restart file + +- if(ltad.or.lbpd)call hyper_close(idnode,mxnode,natms,nsteql) ++ if(ltad.or.lbpd) ++ x call hyper_close(ltad,idnode,mxnode,natms,nsteql) + + c close output channels + +@@ -945,10 +965,7 @@ + endif + + c terminate job +-CVAM +-CVAM call VTEND(99, ierr) +-CVAM +- ++ + c PLUMED + if(lplumed) call plumed_f_gcmd() + c PLUMED +--- dlpoly-2.20.diff/srcmod/basic_comms.f.preplumed.orig 2016-12-01 11:17:21.148368366 +0100 ++++ dlpoly-2.20.diff/srcmod/basic_comms.f.preplumed 2016-12-01 11:17:28.908143066 +0100 +@@ -4,14 +4,10 @@ + c + c communication harness initialisation + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -27,6 +23,8 @@ + return + end + ++ subroutine machine(idnode,mxnode) ++ + c********************************************************************* + c + c dl_poly subroutine for obtaining charcteristics of +@@ -37,9 +35,6 @@ + c + c MPI version - t.forester may 1995 + c +-c wl +-c 1.4 +-c Exp + c********************************************************************* + + implicit none +@@ -58,13 +53,9 @@ + c + c routine to determine identity of processing node + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -86,13 +77,9 @@ + c + c calculate dimension of hypercube + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -122,13 +109,9 @@ + c + c calculate number of nodes + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -150,14 +133,10 @@ + c + c Intel-like csend (double precision) + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -183,14 +162,10 @@ + c + c Intel-like crecv (double precision) + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -223,11 +198,6 @@ + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c*********************************************************************** + + use setup_module +@@ -265,11 +235,6 @@ + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c*********************************************************************** + + implicit none +@@ -305,11 +270,6 @@ + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c*********************************************************************** + + use setup_module +@@ -344,9 +304,6 @@ + c author - w. smith march 1992 + c MPI version - t. forester may 1995 + c +-c wl +-c 1.4 +-c Exp + c*********************************************************************** + + +@@ -371,14 +328,10 @@ + c + c barrier / synchronization routine + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c CPP version - w.smith + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none +@@ -400,14 +353,10 @@ + c + c exitcomms: exit from communication harness + c ++c copyright - daresbury laboratory + c MPI version - t.forester may 1995 + c CPP version - w.smith may 1995 + c +-c wl +-c 2008/01/14 13:33:07 +-c 1.4 +-c Exp +-c + c********************************************************************* + + implicit none diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..2cfa765309fe6b0091a580abbce4d143a9c08b04 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +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': 'iomkl', 'version': '2016.07'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('CMake', '3.4.1'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..215719decbddb8536a0ffb5045ff29806d80f2d5 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('CMake', '3.4.1'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..d5229b92598f28139eba32358e9f511bfa2051a6 --- /dev/null +++ b/easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'dadi' +version = '1.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/gutenkunstlab/dadi' +description = """∂a∂i implements methods for demographic history and selection inference from genetic data, + based on diffusion approximations to the allele frequency spectrum.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://bitbucket.org/gutenkunstlab/dadi/get/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cd %(builddir)s/*/tests && python run_tests.py"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..0b49bfdbc1d21b2a63455b0ed48a0d04cd41c617 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'dask' +version = '0.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '2.7.12')] + +exts_list = [ + ('toolz', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + }), +] + +# 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 = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..46b06c2e96c2cc50fe79f5a5370ffd3c8b738fd1 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'dask' +version = '0.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '3.5.2')] + +exts_list = [ + ('toolz', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + }), +] + +# 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 = 'data' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3d05e04fc17aa8fa19504d5b2de0b4a77d6b5ccd --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.106' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('DBus', '1.10.8'), + ('expat', '2.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..318a8a890a3ed9ad552a883b787e5674c5e6e423 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.108' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('DBus', '1.10.12'), + ('expat', '2.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e72d5ec347180e19e815b0820e5ad346631d4cb --- /dev/null +++ b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'distributed' +version = '1.14.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://distributed.readthedocs.io/' +description = """Dask.distributed is a lightweight library for distributed computing in Python. + It extends both the concurrent.futures and dask APIs to moderate sized clusters.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('dask', '0.12.0', versionsuffix), +] + +exts_list = [ + ('zict', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + }), + ('HeapDict', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], + 'modulename': 'heapdict', + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('tblib', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + }), + ('psutil', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'source_tmpl': 'psutil-%(version)s.zip', + }), + ('msgpack-python', '0.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], + 'modulename': 'msgpack', + }), + ('locket', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], + }), + ('cloudpickle', '0.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + }), +] + +# 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/dask-remote', 'bin/dask-scheduler', 'bin/dask-ssh', 'bin/dask-submit', 'bin/dask-worker', + 'bin/dcenter', 'bin/dcluster', 'bin/dscheduler', 'bin/dworker'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..82253f9f50d4e1685c22dfdab7aa01b6cb747254 --- /dev/null +++ b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'distributed' +version = '1.14.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://distributed.readthedocs.io/' +description = """Dask.distributed is a lightweight library for distributed computing in Python. + It extends both the concurrent.futures and dask APIs to moderate sized clusters.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('dask', '0.12.0', versionsuffix), +] + +exts_list = [ + ('zict', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + }), + ('HeapDict', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], + 'modulename': 'heapdict', + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('tblib', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + }), + ('psutil', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'source_tmpl': 'psutil-%(version)s.zip', + }), + ('msgpack-python', '0.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], + 'modulename': 'msgpack', + }), + ('locket', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], + }), + ('cloudpickle', '0.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + }), +] + +# 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/dask-remote', 'bin/dask-scheduler', 'bin/dask-ssh', 'bin/dask-submit', 'bin/dask-worker', + 'bin/dcenter', 'bin/dcluster', 'bin/dscheduler', 'bin/dworker'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..653bc39a36da765a127f8b355f1ed1b137302d95 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb @@ -0,0 +1,46 @@ +# 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 + +# Provided binaries required OpenBLAS and GSL libraries + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '6.0.1' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/' +] +sources = ['EIG%(version)s.tar.gz'] + +dependencies = [ + ('GSL', '2.1'), +] + +# -lm and -pthread are missing in the Makefile +# also run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl $LIBBLAS -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' + +start_dir = 'src' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..90343733e32df8004690e03412fe9e120e5b5702 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -0,0 +1,46 @@ +# 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 + +# Provided binaries required OpenBLAS and GSL libraries + +easyblock = 'MakeCp' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/' +] +sources = ['EIG%(version)s.tar.gz'] + +dependencies = [ + ('GSL', '2.1'), +] + +# -lm and -pthread are missing in the Makefile +# also run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl $LIBBLAS -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' + +start_dir = 'src' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.0.0b36-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/e/ETE/ETE-3.0.0b36-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..c349cc7f20ec5a086ed7397a1f93bb52f747c9b9 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.0.0b36-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.0.0b36' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/etetoolkit/ete/archive/'] + +dependencies = [ + ('Python', '2.7.12'), + ('lxml', '3.6.4', versionsuffix), + ('PyQt', '4.11.4', versionsuffix), +] + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..09a04b73a8f427188cb2bc3f7e346eeb00d98ebf --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.9.0' + +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/0e/83/4ed8215c5b27ba4ee4a6da3d43ce9579b67c5fe7a91f33f48991f878db13/', + # vsc-base + 'https://pypi.python.org/packages/2b/fd/e16d723389f692b107b5e4e6243379d2b056e79a7ea3b5e4fdc2753d9541/', + # easybuild-framework + 'https://pypi.python.org/packages/e9/c7/da05d522cfc8b932956e77bdbf5270a91443df1f91bc2004a08776bd55da/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/0f/c4/65f98c2dc041e8201a51d2be61ec407e421f02e4f43775c7cb85ed4b8bcd/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/0a/5e/a0faffd999833c9f745b0f5592a8bce51556a4604d90daeda024244fa6fe/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.15.tar.gz', + 'vsc-base-2.5.4.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-3.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a77b43aaad9574d1e07c246452364acbd747d106 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.0.0' + +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/4a/1c/abb1bcd09523a7c9d52e2703f67dec4807751674c13be17e89a7602677b0', + # vsc-base + 'https://pypi.python.org/packages/73/24/e4244a743e0cfc4af1f3b3b772698e2f4dafc7052bc006a1b829b66f7a3a', + # easybuild-framework + 'https://pypi.python.org/packages/14/5f/1112f3870891992e3c01db8202f913d61577e70975a371c3fd956b9a6b11', + # easybuild-easyblocks + 'https://pypi.python.org/packages/07/e3/68ec2ff700a25a44b51ee45dd28d21352286b384d77b70cfe6dde1db6e28', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/f3/6c/60625b79a2613d229834e7920fa91eebf92cba77ec18bdca0ae2bfd4c99a', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.19.tar.gz', + 'vsc-base-2.5.5.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3d9fd925081d44fddc3ea4e86387e07c21a9e64a --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.0.1' + +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/9c/fa/648c7484cef36f752a41f7a3d8ef1db7ed7741b0440eae87694b7de835ae', + # vsc-base + 'https://pypi.python.org/packages/73/24/e4244a743e0cfc4af1f3b3b772698e2f4dafc7052bc006a1b829b66f7a3a', + # easybuild-framework + 'https://pypi.python.org/packages/78/63/d0d2cc49885c1fa86bdbbf3c3a314526fe4d7ddd43fa79b6b41fdd959ede', + # easybuild-easyblocks + 'https://pypi.python.org/packages/0b/36/9b492be00eb4f0ac229ccba354bc5c327cbbf590be85f4d996a40ce956b6', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/5b/d2/6f9a02af09c77adc19176227657a313eb06eb28faf0372ca6dead231404d', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.20.tar.gz', + 'vsc-base-2.5.5.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2016b.eb new file mode 100755 index 0000000000000000000000000000000000000000..66e4f6f45ff04e834d4b451819762e8f2df87ba4 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.3' + +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': 'foss', 'version': '2016b'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016b.eb b/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2db42a61e2e8902037c093c754679a3901bfb11 --- /dev/null +++ b/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016b.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'Elk' +version = '4.0.15' + +homepage = 'http://elk.sourceforge.net/' +description = """An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with +many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the +EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that +new developments in the field of density functional theory (DFT) can be added quickly and reliably. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TGZ] +source_urls = [SOURCEFORGE_SOURCE] + +checksums = [ + '760623faf5aab9b1f49488edbaae65fb', # elk-4.0.15.tgz +] + +dependencies = [ + ('libxc', '2.2.3'), +] + + +# make.inc file is generated interactively by "setup" command, creating it here +prebuildopts = 'echo "F90_OPTS = $FFLAGS" > make.inc && ' +prebuildopts += 'echo "F77_OPTS = $FFLAGS" >> make.inc && ' +prebuildopts += 'echo "LIB_LPK = $LIBLAPACK" >> make.inc && ' +prebuildopts += 'echo "LIB_libxc = $EBROOTLIBXC/lib/libxcf90.a $EBROOTLIBXC/lib/libxc.a" >> make.inc && ' +prebuildopts += 'echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_FFT = zfftifc_fftw.f90" >> make.inc && ' + +buildopts = 'all' + +parallel = 1 + +files_to_copy = [(['src/elk', 'src/spacegroup/spacegroup', 'src/eos/eos'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/elk', 'bin/spacegroup', 'bin/eos'], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f186cddd62fc655bd7a79f1c1554ce9af52e4452 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.49.5')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7cf3821ef383af5885f474a2889e58a3b9f0cdbe --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'ea-utils' +version = '27a4809' + +homepage = 'https://code.google.com/p/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': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] +sources = [SOURCE_TGZ] + +checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] + +start_dir = 'clipper' + +prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " +buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' + +builddependencies = [ + ('Perl', '5.22.1'), +] + +dependencies = [ + ('GSL', '2.1'), +] + +files_to_copy = [([ + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' +)] + + +sanity_check_paths = { + 'files': [ + 'bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall' + ], + 'dirs': [] +} + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8447b7c643d41508383b06f62954f8c177a572e --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'ea-utils' +version = '27a4809' + +homepage = 'https://code.google.com/p/ea-utils/' +description = """Command-line tools for processing biological sequencing data. +Barcode demultiplexing, adapter trimming, etc. + +Primarily written to support an Illumina based pipeline - +but should work with any FASTQs.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] +sources = [SOURCE_TGZ] + +checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] + +start_dir = 'clipper' + +prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " +buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' + +builddependencies = [ + ('Perl', '5.22.1'), +] + +dependencies = [ + ('GSL', '2.1'), +] + +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/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..af5414eaac6f71f27a3ae2af24b19f09c4a5ae9a --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.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': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), + ('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/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef4b99cd73049f0d85929e161e63245d1cb32c4e --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb @@ -0,0 +1,47 @@ +## +# 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 +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['fastx_toolkit-%(version)s.tar.bz2'] + +builddependencies = [('libgtextutils', '0.7')] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..477d5d84f28f6a947e5624d2aa89e75426214146 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.5.2' + +homepage = 'https://pages.nist.gov/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['Git-r21.tar.gz'] + +patches = ['FDS-r18915_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} + +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..3fd16df92fc0b3f4729925930cd12755429582ad --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +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': '2016.07'} +toolchainopts = {'optarch': True, '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'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb new file mode 100644 index 0000000000000000000000000000000000000000..283a4b3d0dcfb8bb353a550d1285d7a6d9727d3b --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +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': 'gompic', 'version': '2016.08'} +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'], +} + +moduleclass = 'numlib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..854d665922a217eadea7bf2db6689ea8ea79cf8c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016.07'} +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'], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..95601b61f5bfb09763f66d769050eb2341f2fbcd --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016.09'} +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'], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..e222c97b5d0038b3fc69a5a4e0b300763864bb05 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016b'} +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'], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..2499d7f87ae01192d570649b37573f584fd88ea3 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2016.10'} +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'], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..6fcdd25eb53518ea226ff2cd9566a603bcb73901 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +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 +] + +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'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb new file mode 100755 index 0000000000000000000000000000000000000000..e96e5e3b33d5f69270562508cd3145ce369d604a --- /dev/null +++ b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FFindex' +version = '0.9.9' + +homepage = 'http://www.splashground.de/~andy/programs/FFindex/' +description = """simple index/database for huge amounts of small files""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.splashground.de/~andy/programs/FFindex/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +start_dir = 'src' + +buildopts = 'USEMPI=1' +installopts = "USEMPI=1 INSTALL_DIR=%(installdir)s" + +runtest = 'test' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ffindex_%s' % x for x in ['apply', 'build', 'from_fasta', 'get', 'modify', 'unpack']] + + ['lib64/libffindex.a', 'lib64/libffindex.so'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb index 3e71d0c50e397537dd12a800a5347be195714c09..36e057b4695d683b66d84f4abfc779743ae6692a 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb @@ -16,7 +16,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.11.08'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160114'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -25,7 +27,7 @@ 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 ['so', 'a']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb index 40be8fe314c14e52eef4182c3fc91ac890a1a076..3349ed39612bc967a897291626338d0eb9469ced 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.11.08'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160114'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -23,7 +25,7 @@ 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 ['so', 'a']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb index 0badebf4eb9eac06b609ce7704baaf1e3293e081..866438750623e5ac55bbc2b0555fb73a5af9db71 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb index 05478ccadaa7fcaad792c1fee2c2dd065061c646..c6c61c7b359b42e2e9e89e06dab4f8d2a526af68 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -23,7 +25,7 @@ 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 ['so', 'a']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4eee74c06297b3adca9dd787f0ce487d2d7a96b0 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('x264', '20160430'), + ('libxcb', '1.11.1'), +] + +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/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb index fb0c75a29bf506b5f2c2f3bc0c2fa9bead429a0a..fd22efefe030d73a18745f0dad526c98ec0ae245 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -23,7 +25,7 @@ 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 ['so', 'a']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb index 4dee167c84a56e381677064a4947aa30e9985d61..0744eae109c4a859e10e10a188cebb3f7c912b95 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -14,7 +14,9 @@ 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" ' @@ -23,7 +25,7 @@ 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 ['so', 'a']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FGSL/FGSL-1.1.0-intel-2016b.eb b/easybuild/easyconfigs/f/FGSL/FGSL-1.1.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e06458da7eb737a6d96e4f4bc6b5de7fcdfa770e --- /dev/null +++ b/easybuild/easyconfigs/f/FGSL/FGSL-1.1.0-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FGSL' +version = '1.1.0' + +homepage = 'https://www.lrz.de/services/software/mathematik/gsl/fortran/' +description = """FGSL: A Fortran interface to the GNU Scientific Library""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/reinh-bader/fgsl/archive/'] + +dependencies = [('GSL', '2.1')] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] + +preconfigopts = 'autoreconf -fvi && ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libfgsl.%s' % SHLIB_EXT, 'lib/libfgsl.a'], + 'dirs': ['include/fgsl', 'lib/pkgconfig'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb index 0056b1139192bd5799d888a349a75faf2c3c2398..228b99e49ee8fd4060c9b3574122997ddbeae6c2 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb @@ -17,6 +17,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c82344219b57943b028a5c2334c4503dfe42bf9 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb @@ -0,0 +1,38 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('xprop', '1.2.2'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index d88b64d96a2da3e6b80862b404dd8d9b8273843d..efbb3a22823b48408dc53f61d823ea441c66aa11 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -17,6 +17,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a909b40155ead2bca8e804bf6fd35d269e76653 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb @@ -0,0 +1,38 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('xprop', '1.2.2'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch new file mode 100644 index 0000000000000000000000000000000000000000..5ddc1900edaf276acda446e3a5bc07e5c64a73b1 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch @@ -0,0 +1,46 @@ +#see https://groups.google.com/forum/#!topic/fltkgeneral/GT6i2KGCb3A +#and http://www.fltk.org/str.php?L3156 +# GNU Octave compains: +# error: octave-4.0.3/libinterp/dldfcn/PKG_ADD: octave-4.0.3/libinterp/dldfcn/__init_fltk__.oct: failed to load: FLTK/1.3.3-intel-2016b/lib/libfltk_gl.so.1.3: undefined symbol: _ZN18Fl_XFont_On_Demand5valueEv +Index: src/fl_font.cxx +=================================================================== +--- fltk-1.3.3/src/fl_font.cxx (revision 10503) ++++ fltk-1.3.3/src/fl_font.cxx (revision 10504) +@@ -55,6 +55,12 @@ + # include "fl_font_x.cxx" + #endif // WIN32 + ++#if ! (defined(WIN32) || defined(__APPLE__)) ++XFontStruct *fl_X_core_font() ++{ ++ return fl_xfont.value(); ++} ++#endif + + double fl_width(const char* c) { + if (c) return fl_width(c, (int) strlen(c)); +Index: src/gl_draw.cxx +=================================================================== +--- fltk-1.3.3/src/gl_draw.cxx (revision 10503) ++++ fltk-1.3.3/src/gl_draw.cxx (revision 10504) +@@ -81,7 +81,7 @@ + * then sorting through them at draw time (for normal X rendering) to find which one can + * render the current glyph... But for now, just use the first font in the list for GL... + */ +- XFontStruct *font = fl_xfont; ++ XFontStruct *font = fl_X_core_font(); + int base = font->min_char_or_byte2; + int count = font->max_char_or_byte2-base+1; + fl_fontsize->listbase = glGenLists(256); +Index: FL/x.H +=================================================================== +--- fltk-1.3.3/FL/x.H (revision 10503) ++++ fltk-1.3.3/FL/x.H (revision 10504) +@@ -132,6 +132,7 @@ + XFontStruct *ptr; + }; + extern FL_EXPORT Fl_XFont_On_Demand fl_xfont; ++extern FL_EXPORT XFontStruct* fl_X_core_font(); + + // this object contains all X-specific stuff about a window: + // Warning: this object is highly subject to change! diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1ec088d35eb90f8cbc7d7876e93e40a1fee5970 --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb @@ -0,0 +1,14 @@ +name = 'FLUENT' +version = '17.1' + +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 = ['FLUIDS_171_LINX64.tar'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..807f2d8eb84958f3bf25c7db5240bceb5abf2855 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.19' + +homepage = 'http://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] + +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.py *.pl train example' + +files_to_copy = ['FragGeneScan', 'FGS_gff.py', 'post_process.pl', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FGS_gff.py', 'FragGeneScan', 'post_process.pl', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb b/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0fc7d99c552bc3695911d0cb39fc8de764dd1b4 --- /dev/null +++ b/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'f90cache' +version = '0.96' + +homepage = 'http://people.irisa.fr/Edouard.Canot/f90cache/' +description = """f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, + using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. + This often results in a great speedup in common compilations.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://people.irisa.fr/Edouard.Canot/f90cache/'] +sources = [SOURCE_TAR_BZ2] + +buildopts = "CFLAGS='-O2 -static'" + +sanity_check_paths = { + 'files': ['bin/f90cache'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb b/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..51d81cd7106301839a7ecc73d64716473049861c --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.28' + +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': 'foss', 'version': '2016b'} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..06eb1f492ad91428703d5e71818366c181b97f84 --- /dev/null +++ b/easybuild/easyconfigs/f/findhap/findhap-4.eb @@ -0,0 +1,38 @@ +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'findhap' +version = '4' + +homepage = 'http://aipl.arsusda.gov/software/findhap/' +description = """Find haplotypes and impute genotypes using multiple chip sets and sequence data""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(name)sV%(version)s.zip'] +source_urls = ['http://aipl.arsusda.gov/software/%(name)s/'] + +modextrapaths = { + 'PATH': '', +} + +modloadmsg = """ +Copy the following file to the directory from which you will be running the executable: +\\$EBROOTFINDHAP/findhap.options + +Other files in the \\$EBROOTFINDHAP directory are: + +\\$EBROOTFINDHAP/genotypes.txt +\\$EBROOTFINDHAP/chromosome.data +\\$EBROOTFINDHAP/pedigree.file +\\$EBROOTFINDHAP/sequences.readdepth +""" + +sanity_check_paths = { + 'files': ['findhap4', 'findhap4.f90', 'genotypes.txt', 'chromosome.data', 'pedigree.file', 'sequences.readdepth'], + 'dirs': ["Example_Output"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb index 24e3dfb5dc336b8cad4e650054195077c7496dce..0542fac499fc9656f2973ce27f30a9b5091371a4 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb index 8c57faa30991446979874b6897cd22216ae6b6b3..ce034a2f5d487b076325014299320f5dbe2533f1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index 98e5ff55276e13009f98c7b0bc1de298dae26f1b..ac2d9ea1647105ebe9fa00ad52d25cae5a6902c2 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -6,10 +6,16 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb index 1c15e90f19802698bd652fedb19559f92f98f91a..6e01f166de9837fd871dae6e3464e376b0ca982c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb @@ -6,8 +6,15 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 667f205b6954315caf061213eac9a4b997c25c0b..72d2805b5fefb17aa60273349294dd9ea43cacfb 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -6,10 +6,16 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb index 034599b7bc3de6886532e66e3a52affef9b6bfe7..d5baf97d6dd6880886eaa4f8ac6b5e7a18bed5c6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb @@ -6,8 +6,15 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index 75d18ede78430340ae8f7496931339f6e688b5f6..facf8e7f13dafe0653bf4cb9ecaf36edacd19a8c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -6,10 +6,16 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb index 71675a8b5cf7215ebdc4aa4a09783a1e834e7e93..a28470817bb2799f6b748e271d4aeb331add1218 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -6,14 +6,17 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCCcore', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -# use same binutils version that was used when building GCCcore toolchain -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.25', '', True) +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] +dependencies = [('M4', '1.4.17')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index 32dffb057fd38fb79e7dfdf93bb6fe6652af369e..68344b21cb34ee7ea5c26f090638d1e0c9f03883 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -6,14 +6,17 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -# use same binutils version that was used when building GCCcore toolchain -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.25', '', True) +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] +dependencies = [('M4', '1.4.17')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb index 3b653b0adc02af1583620de8c7e2890692646f32..255450ebc92082562cae3b92924b3c6f6312394e 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb @@ -6,8 +6,15 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb index 6a24b017aa79cbb8a179bb5730ccdb950543b29b..72f37c4db66e8a31db0a08358bb422cbbbe38d12 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 208a02e5403e45baf0640fa33ec53981b1c802b5..1ad0409c77de1f8bc4e8fe9d74364b81b8d67b03 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb index f9226ff5f3631f67338c0176482e53e3ed58e4e3..11968e16401e750fde76e4cd8c1f807837e54c5e 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb index 40befb9e4a6c8fb35ce9eded5398b2f5d0a6366b..3f2d3b24f604d72242fd26a754a0a4bce9cc8394 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb index 352bff833483b41833a9c2adf3263328bfcc34d2..69470ed39aae38e053cbdbb27c92ac25bd38e228 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb index 0bebc7206722a53faeb78cf5c656d06514ad8ce1..60bcff5315cd37406a29ed29887c29b5da9f7924 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb index dc6e43a06efd405a2d7e998c1fc1843b3af8f2b0..0f6d234b9e793555bcb48532e39b83fac8ee5962 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb index a2a804a3796434f6b2a46eb1c72cf4b130fc7821..37e678754d0841b52a42cb9c63414a3d6491d5a9 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb index 859df835438604c2d657d943debec8a1e071b57f..7f2ee18cbd580a934d4b013ede7ec8f5fdde0fdf 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb index 159eef32748c5e16b8928678a2ff6c851f0bb487..cc528417f16809f377e62139185d7734c91c3f11 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb index 154963c1c85cc6f2b946d83fb270a96e19cb018c..5e00cb4b9a8a247d84de075c83e2cf11f8962710 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb index 419266740d48f770220ab36af19b4eea900c0fea..de60e46854caf04f0d286849c4c7e765ca3ee619 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d599b0583d028c7a85abfab252d3edc227005c1c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb index e4d83f163cb9c7b974e70a586251f06ef412e697..797f2faa4fd20a68551696ad0b0e3f6836069af6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -builddependencies = [('M4', '1.4.17')] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb index 3626cfd2399a402a902c8c3729d6b01632c4b2e8..96c99f1d3c7e275c8ca6e3d05941f3a590aa142c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 4015f4129186587d66c5fad9158d35c5a271c6c4..b7b82f91973a0c140afceec9c9952c581e024ecd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -11,11 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] - -parallel = 1 +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 0b38c37169cf03232e7816dc82c569a1bb93c385..73279c6d88cda5d1c4c3718ac303fc9c8411b714 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -11,11 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] - -parallel = 1 +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index e1a943777464a69db10ab7b224b2bd5116257f58..954dea0d03b4b48ff58a7d2669392156aef70eca 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -11,11 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] - -parallel = 1 +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # 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-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index 299747415ee51dbf81f0ed048d0d9bb390c5560f..ee9b4ed94d327a92a7790ff9c4a29749d6fd7022 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -11,11 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] - -parallel = 1 +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # 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-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..51d6c9f7b63df894c17190e0afbf070167bc9c5d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -0,0 +1,25 @@ +name = 'flex' +version = '2.6.0' + +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': '6.1.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # 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-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 76aba74a8b0af8df0b0dcc5f992f473ac2d8ef71..43cfdfac42c2c9b7aba940b18f55419747ae4864 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -11,11 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] - -parallel = 1 +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # 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-2.6.0-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb index bd783441d3334e3add6192d730197dc1c0c64441..5c0eb6b59ddcb6d4f19406d45e852777b7d32d39 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb index 13ec4d5ea65f82f531926b869fa1ff7f4c8037ef..415a80ac0496acd51823bdf0de5db06fb496d6f1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb index a59cd4005e342973711ed95e0ae00e6d478e8832..626ebe5d467e8970022cfc467f89bfb3440f634e 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb index c2677565b597dedb7ead661f16ed06c8aa7aafb0..3d60cee6749bd6adbef9a291eba0798322f86d0d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb index c3e7a6b9650d13a062783d2844ab2e24b351b01d..098c6168e74256498c2ea16b002d3d5d6e358a71 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb index f451c3ed904166bda6cbe3f0133aa5173eae284c..da18a622381bff83d4b218c4fb1e30eb1571faa3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb index 39937675eb0a18bba0cfed153d53591f17dd50b8..1dc06e55c18c1bac16123fb3ece39831dd5ea2c1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.07.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..783366f34ad752c7a388372798163ab6f3eeebb0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.07.eb @@ -0,0 +1,17 @@ +name = 'flex' +version = '2.6.0' + +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..a3d444f9dec0b3f9d042c49014b6f4b8cbb99372 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +name = 'flex' +version = '2.6.0' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb index e7580df4ae2d27389ac5ad52e49caf6295a1b414..853b81ad96d86c93d47dba29560b68a5731b9faa 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz +] + +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ac6504cacf54b1ffc819ce1d2b7bb7d5ca30be92 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb @@ -0,0 +1,22 @@ +name = 'flex' +version = '2.6.2' + +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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['cc6d76c333db7653d5caf423a3335239'] + +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..be4b4394550972b1e5cbdb9885079ffbdd68d56e --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.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': '2016b'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.6.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.07.eb b/easybuild/easyconfigs/f/foss/foss-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..052846a744362431d01f02132bbe39bad71b5161 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.07.eb @@ -0,0 +1,37 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.07' + +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 = '6.1.0' +binutilsver = '2.27' +gccbinver = '%s-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.1' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccbinver), + ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc) +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.09.eb b/easybuild/easyconfigs/f/foss/foss-2016.09.eb new file mode 100644 index 0000000000000000000000000000000000000000..89b1d4573215ac72719e86267198edf8f91170fb --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.09.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.09' + +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 = '6.2.0-2.27' + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.1' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.5', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc) +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ccad2796aa14d16e742fd06d511c3f702f62e7e5 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb @@ -0,0 +1,34 @@ +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': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.6.1')] + +dependencies = [ + ('X11', '20160819'), + ('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-2.6.5-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9156052c8f80538dcf9e207ebefbcb55813a513e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.6.5' + +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': 'foss', 'version': '2016b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.24'), + ('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/f/freetype/freetype-2.7-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b88736d00a0a14b914b4b41faa4f86a02d997dc --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.7' + +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': 'foss', 'version': '2016b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.26'), + ('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/f/freetype/freetype-2.7-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..52d8477931111ad36d7bd096d4f45f8b0e8ad9a6 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.7' + +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', '1.6.26'), + ('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/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 97ecab725e60db03bea4b939a16922fc2e32cc58..041898fae9be81ec8e4fed61e6d9aa5acde12186 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -16,6 +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 ] sources = [ SOURCELOWER_TAR_GZ, @@ -41,7 +42,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb index 18a5c26a0427e09729a7f50f58eb2ef181bd930b..85085960e869e77f517cdfc7091cc86e9f623ed8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 0cc4d2d8be7fd389ad7f0f79e211783994c5f7d7..91e4497eaa3ab6dd231e2bb082ac752f395f66ef 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 @@ -16,6 +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 ] sources = [ SOURCELOWER_TAR_GZ, @@ -43,7 +44,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 76ee08688ea2fedc67abd1ba8836775d2e8592c8..d6ce9a89a02113ec336fbb9c175675d4f79eb2f9 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -16,6 +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 ] sources = [ SOURCELOWER_TAR_GZ, @@ -41,7 +42,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb index 45168e2586049545e95a7d8100e84346bd09488c..8154896aaaf51e58bdf4e6af8db24499a4a523bf 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb @@ -32,7 +32,4 @@ languages = ['c', 'c++', 'fortran'] multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb index 4f8e1b941b4ef5502a0585f5a97db7b87b04a204..525d8bbaf403b4b595476e6e1a609c1a2abe46cb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 8f71a86f5fe50f2f1633194f33cc76ce883f0f37..a5d4cd082d2dd99b8412b653384c7c00238db55c 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 @@ -16,6 +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 ] sources = [ SOURCELOWER_TAR_GZ, @@ -43,7 +44,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb index 10a1ebfca0c13c269c9ce0edca35ffe4cf6b869e..d300b36d8f4abd51f8fde9cdbbcb710e47b7360a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 a553c070ef35f4726333b0b2ecabc1953763ffc7..1d2159779bce34205d43f6c2dc33c7bf4f5d276b 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 @@ -16,6 +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 ] sources = [ SOURCELOWER_TAR_GZ, @@ -43,7 +44,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 7dd0f5df2417eeb5b9f4373e2dc5e7a7d4dbdc16..bcc4336300082b7fc8249dd2ac7ee16aa1391d22 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -16,6 +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 ] sources = [ SOURCELOWER_TAR_GZ, @@ -41,7 +42,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb index 5ac47478fb0e9e75882bc0cca3d08b3b8bce0976..5149d85b529355ff3d0a09bdc9cf4266fbd331cb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb index 861866153237fa8bb6e7c9ada3237e0589fe83ad..358952fcd93440f78f5bd69cfcdf78f04c75f0a0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 f77a70efc324adf52046ce3c70c4debc33c16a13..1293532d231ecea5f29ba4cdcbfe250ff3427850 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 @@ -18,6 +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 ] sources = [ SOURCELOWER_TAR_BZ2, @@ -48,7 +49,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 9974833bba59a31a3f63ff7cf7e6eba06bcedb9a..82341a9a29ac9944ea4d4df5754b29cd8d047325 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -18,6 +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 ] sources = [ SOURCELOWER_TAR_BZ2, @@ -46,7 +47,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb index cd09534c392e7c40d452193bba441f07b3990c9b..288754285b5fc3188f8b0b99b631a50a785c1e54 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 a3c67d644eca470aae379d1cf124de3222358c56..7f03450a91d6c6dadc28f4a9c2ce6c6d45ed8e6a 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 @@ -18,6 +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 ] sources = [ SOURCELOWER_TAR_BZ2, @@ -48,7 +49,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 b78ac53014e98c0fed32e19b1080e14a0a4dac48..163de21ca1ef78b62227539954adaf7e898aca81 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -18,6 +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 ] sources = [ SOURCELOWER_TAR_BZ2, @@ -46,7 +47,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb index 21e41342d35f8697a93033cd5585affafb06680a..d520b55ace0ec67bce667f284b5320d3897e8606 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 0906283ab2eeb69d0de701fe2961f588b61c5bd9..323622921da5f3a903b3fd6bdd6091b7cd62640b 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 @@ -18,6 +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 ] sources = [ SOURCELOWER_TAR_BZ2, @@ -48,7 +49,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 1af6bd9c365216d2a784bb27bec01b94dd952e57..b5769a1078543d0594ded3d4238dbbb2ef3d89a3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -18,6 +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 ] sources = [ SOURCELOWER_TAR_BZ2, @@ -46,7 +47,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb index 4985b9228e2dc28a36621c2abb6330005889afa0..44e39d233dbce4c9893ed772eaab89aca95e59a1 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -39,7 +39,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index cb9f3aa4f229fc45b33965ec6cc89e9850de59f8..e9df0050c041397c2f8ff48cbe11f1fbbd8e00b1 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb index d762426d0618730787e39f334cdde95902342b52..8c62c139203918cb14e9cada43fafc3495ebb668 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -39,7 +39,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index 759f134bcc6554ea09caed6b0eb0282658430714..e36af87104969d95f12581b321fe5cbf3403daf4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' 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 8bbf0ea88e7755cbc48981ead7cadf5f0b405f6b..4820fd10264616e3eeb13b35b9a97731701c94f5 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 @@ -19,6 +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 ] sources = [ @@ -49,7 +50,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index a69c58da2c59ea2dbfd2013b502eab93a8e43b60..f18257966453036dd089bc6a3a52466fa1969951 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -16,6 +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 ] sources = [ @@ -43,7 +44,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index c25b63f7b1fd3d926eda88ef886de6f153214890..47b8d2c23ba4ce8fb2ae5b3a6e6e36b821d16906 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -16,6 +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 ] sources = [ @@ -43,7 +44,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index 83ebb4cb78dc3d2bf23d1c15f2127d44fed2de6e..3aa9d513bb90d1e82d97033e0c11ab4537f5917c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -16,6 +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 ] sources = [ @@ -43,7 +44,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..4faa0a48e88c2ccca189c320cebacabd6aab284f --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.1.0' + +binutilsver = '2.27' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb index 01f4776c64c4627f65b18f7407d6c2bc3d3c22ab..872c6745e01b97bcb014ce11fc90d456d6e75f45 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -42,7 +42,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index a4f11a8fbdad1938453a02d2e5f7b788de3cdc5b..d0d9f1d3a7d8ab5afeccff1adc610a1f24aa20b1 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -41,7 +41,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb index 1a8e12a57a60f46e99562989fd2cf03ee5f15d46..9a01aa75efb41c142b97c6e3b04ab782731b4dcb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb @@ -41,7 +41,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - 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 1f2fc04edbe382762c3f9effff81cf3c4d7f1c5e..4998bcfabac4afb5a3760c1359e1894430b3aaba 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -18,6 +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 ] sources = [ @@ -48,7 +49,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 5b9a17485e0b1e0ea8b55fe34c5700270ae8a7dc..2a3fe7ab858abc680f75b5682a17e7da6b2573ec 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -18,6 +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 ] sources = [ @@ -48,7 +49,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..603dbd6cc5e555d8201212fb2b0f0fbc80532080 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -0,0 +1,55 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '6.1.0' + +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 = '3.1.4' + +source_urls = [ + '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://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 +] + +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-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + ('%s-%s_fix-find-isl.patch' % (name, version)), +] + +checksums = [ + '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 + '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 + 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.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-6.1.0_fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_fix-find-isl.patch new file mode 100644 index 0000000000000000000000000000000000000000..6334b6be3527921cba381caf0277f360482d93cf --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_fix-find-isl.patch @@ -0,0 +1,14 @@ +# Don't use libmpc and libmpfr to find libisl +# by wpoely86@gmail.com +diff -ur gcc-6.1.0.orig/configure gcc-6.1.0/configure +--- gcc-6.1.0.orig/configure 2016-08-26 17:51:48.470524515 +0200 ++++ gcc-6.1.0/configure 2016-03-17 23:54:19.000000000 +0100 +@@ -6018,7 +6018,7 @@ + _isl_saved_LIBS=$LIBS + + CFLAGS="${_isl_saved_CFLAGS} ${islinc} ${gmpinc}" +- LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs} ${gmplibs}" ++ LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs}" + LIBS="${_isl_saved_LIBS} -lisl -lgmp" + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for isl 0.16, 0.15, or deprecated 0.14" >&5 diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 011920e0f4ee82b69dd08c3dfc10a882ed32f547..5b1200a09b5adb9149160ef4f7b7b90839d8cc4c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -12,12 +12,13 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + '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 = [ @@ -50,7 +51,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b42d8e1b61951e910fa8de90602815402ce47d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.106'), + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('libxml2', '2.9.3'), + ('GTK+', '2.24.30'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a184de7e11e3abfe4f04de17b665ba49a762a573 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.108'), + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1'), + ('libxml2', '2.9.4'), + ('GTK+', '2.24.31'), + ('intltool', '0.51.0', '-Perl-5.24.0'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ec6ce953ae72d20e8716c2f5ef3b5cbef5ee576 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.1' + +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': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.4.0'), + ('expat', '2.1.1'), + ('libxml2', '2.9.3'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016b.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1afefc8e7263edc409979defb441a63f7217199e --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-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': 'intel', 'version': '2016b'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.6.1'), +] + +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/GLPK/GLPK-4.60-intel-2016b.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..66b0f5b8f26455ebcf27155b679333939bb7b2b7 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.60' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.1')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000000000000000000000000000000000..3e8dd8b2dfa13acd6e43ae320f2a4b53369f24d2 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.49.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8'), + ('libxml2', '2.9.4'), + ('PCRE', '8.39'), +] + +builddependencies = [('Python', '2.7.12')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +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-2016-11-07-foss-2016b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a8ca27958e85ffec8898897a2a72482c79457f0f --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-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 +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2016-11-07' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# 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' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..e34edcb7afd1ae2f6d9401f6aef1c26df5903360 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +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': 'iomkl', 'version': '2016.07'} +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/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a0888eaf0bc27410f21a0472e8ba0d397f1e3e3 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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/GMP/GMP-6.1.1-foss-2016.04.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..81653e7d61ed7d4f6e7a00ca79cb0cd51d6fe10a --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016.04.eb @@ -0,0 +1,30 @@ +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': 'foss', 'version': '2016.04'} +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-intel-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..09a8cb39dc660d306b6d1080bb36d6dc112bc0f7 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-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': 'intel', '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/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec4f6977d05cef703c3fe392587827319b0e0487 --- /dev/null +++ b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,42 @@ +easyblock = 'Bundle' + +name = 'GRIT' +version = '2.0.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nboley/grit' +description = """GRIT - A tool for the integrative analysis of RNA-seq type assays""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('pysam', '0.9.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pysam/'], + }), + (name, version, { + 'source_urls': ['https://github.com/nboley/grit/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + 'patches': ['GRIT-2.0.5_fix-typo.patch'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/run_grit'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('run_grit', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch new file mode 100644 index 0000000000000000000000000000000000000000..cb33a36d9083d1bfbffbd369acb09c31c5492b60 --- /dev/null +++ b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch @@ -0,0 +1,15 @@ +fix typo resulting in AttributeError, see also https://github.com/nboley/grit/pull/3 +author: Kenneth Hoste (HPC-UGent) +diff --git a/grit/files/reads.py b/grit/files/reads.py +index 6228a43..a9cc2db 100644 +--- a/grit/files/reads.py ++++ b/grit/files/reads.py +@@ -957,7 +957,7 @@ class PolyAReads(Reads): + if reverse_read_strand in ('auto', None): + if ref_genes in([], None): + raise ValueError, "Determining reverse_read_strand requires reference genes" +- reverse_read_strand_params = Reads.determine_read_strand_param( ++ reverse_read_strand_params = determine_read_strand_params( + self, ref_genes, pairs_are_opp_strand, 'tes_exon', + 300, 50 ) + assert 'stranded' in reverse_read_strand_params diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..f72c224d321db625c991877e842a7b1002c86c7a --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -0,0 +1,35 @@ +## +# 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' +versionsuffix = '-hybrid' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Boost', '1.61.0'), +] + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..1a85f392c79e1103591ef41e40e8698c87608888 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb @@ -0,0 +1,34 @@ +## +# 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' +versionsuffix = '-mt' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Boost', '1.61.0'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..2e153e4c273ff746aa4738f9f7fa4009838071f3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# 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_2012-93.html +# +# Version 5.1.4 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.4' +versionsuffix = '-hybrid' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.4') +] + +dependencies = [('Boost', '1.61.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab660ee95506e4e89bff259094dc42a37736ac03 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# 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_2012-93.html +# +# Version 5.1.4 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.4' +versionsuffix = '-mt' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.4') +] + +dependencies = [('Boost', '1.61.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f7799c269085cb8d2e51304c23e42c3d69dcaa61 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'version': '2016b', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--with-pic' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6708b4036871a33a26c6b6c63d9c33f7de7dcff9 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +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-2.2.1-intel-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a638ab6e5bc76977baae3f61860d573f0ea853e --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'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/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0bab4473443397afbcaf5a28598814169b8f28b --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..743a59e91a75f2f3bab8542aa585f914ac2fd4de --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..248204c8cc0594b51c617a604da19ea6c545d7d2 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '1.8.3' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GStreamer', '1.8.3'), + ('gettext', '0.19.7'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Bison', '3.0.4', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3dddb7ed206ed02efd2b6dc7f01f99bcd27320f7 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('zlib', '1.2.8'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a0214562e2fb427d1f49102f40d9baa59a0b0d93 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1'), + ('zlib', '1.2.8'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..191ac5221649a1be847135f102bee276c095ad96 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.8.3' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2f8ea38ad71b473812f242533750c0df1ce58eb --- /dev/null +++ b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'CMakeMake' + +name = 'GTI' +version = '1.2.0' + +homepage = 'http://www.tu-dresden.de/zih/must/' +description = """A Generic Tools Infrastructure for Event-Based Tools in Parallel Systems.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/gti-release-1.2.0.tar.gz +source_urls = ['http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/'] +sources = ['%(namelower)s-release-%(version)s.tar.gz'] + +patches = ['GTI-%(version)s-missing-unistd.patch'] + +dependencies = [('PnMPI', '1.2.0')] + +builddependencies = [('CMake', '3.0.2')] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DPnMPI_INSTALL_PREFIX=${EBROOTPNMPI}' +buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' + +sanity_check_paths = { + 'files': ["bin/weaver", "include/I_Profiler.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f8cd4f7bed72370ade3d0d83a7ba78d3bc8b51fd --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.30' + +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': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.20.0'), + ('Gdk-Pixbuf', '2.35.1'), + ('Pango', '1.40.1'), + ('GObject-Introspection', '1.48.0'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..78f4ad00b7ac2afd97659e7d57ae944b75bbdbef --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-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': 'intel', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.22.0'), + ('Gdk-Pixbuf', '2.36.0'), + ('Pango', '1.40.3'), + ('GObject-Introspection', '1.49.1'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f2a2533d67c49c8cc34f119dac2050b1ee0e5c1 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.35.1' + +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': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.48.0') +] + +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/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d84597d6248003715a7297a91e51eb831cea5b1 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-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': 'intel', '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-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8612f2848b8bc1e62a5dc53b6ea654e2da393205 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.19' + +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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +sources = ["ghostpdl-%(version)s.tar.bz2"] + +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'), +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..2238d98b96030c1f2bb7e28875c2c22d5c800f76 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -0,0 +1,29 @@ +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': 'intel', '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'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..20888d4d8732e09c3cee1987e8a7e3bb8d583fdb --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.25' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('X11', '20160819'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.4'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('Ghostscript', '9.19'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch new file mode 100644 index 0000000000000000000000000000000000000000..1b8082e74b5f2fb80f90aed4db3bc95e0ed8df93 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch @@ -0,0 +1,13 @@ +#Intel compiler does not understand __has_attribute(attribute +# Oct 24th 2016 by B. Hajgato (Free University Brussels - VUB) +--- GraphicsMagick-1.3.25/magick/common.h.orig 2016-09-05 21:20:24.000000000 +0200 ++++ GraphicsMagick-1.3.25/magick/common.h 2016-10-24 15:03:21.858939448 +0200 +@@ -128,7 +128,7 @@ + # define MAGICK_ATTRIBUTE(x) /*nothing*/ + # else + # define MAGICK_ATTRIBUTE(x) __attribute__(x) +-# if (defined(__clang__) || (defined(__GNUC__) && __GNUC__ >= 5)) ++# if (defined(__clang__) || ((defined(__GNUC__) && __GNUC__ >= 5) && !__INTEL_COMPILER)) + # define MAGICK_HAS_ATTRIBUTE(attribute) __has_attribute(attribute) + # else + # define MAGICK_HAS_ATTRIBUTE(attribute) (0) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index aee7aa31e0d8e0d995475d8ef5b924ed7d4fe7e0..4634a7fb1a95a1f8a07e89db604c85fe00ef9d6a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -46,6 +46,7 @@ patches = [ 'Graphviz-2.38.0_icc_sfio.patch', ] +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' @@ -54,9 +55,14 @@ 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'] + 'dirs': ['include', 'lib/graphviz'] } +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] + modextrapaths = { 'PYTHONPATH': 'lib/graphviz/python', 'CLASSPATH': 'lib/graphviz/java/org/graphviz', diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index 231a5ddb6f76d9f2472c91c66f44d92e3f71e009..c9fd0d8f277a8411f055171586b80acdaa6af7dc 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -48,6 +48,7 @@ patches = [ 'Graphviz-2.38.0_icc_sfio.patch', ] +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' @@ -56,9 +57,14 @@ 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'] + 'dirs': ['include', 'lib/graphviz'] } +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] + modextrapaths = { 'PYTHONPATH': 'lib/graphviz/python', 'CLASSPATH': 'lib/graphviz/java/org/graphviz', diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..50d0e0b4494364117abe9412241a78040c8de096 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.38.0' + +homepage = 'http://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.graphviz.org/pub/graphviz/stable/SOURCES/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('cairo', '1.14.6'), + ('expat', '2.2.0'), + ('freetype', '2.6.5'), + ('Ghostscript', '9.20'), + ('GTS', '0.7.6'), + ('Java', '1.8.0_92', '', True), + ('libpng', '1.6.24'), + ('Pango', '1.40.3'), + ('Perl', '5.24.0'), + ('Qt', '4.8.7'), + ('Tcl', '8.6.5'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('M4', '1.4.17'), + ('SWIG', '3.0.10', '-Python-2.7.12-PCRE-8.39'), +] + +patches = [ + 'Graphviz-2.38.0_icc_vmalloc.patch', + 'Graphviz-2.38.0_icc_sfio.patch', +] + +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " +configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no ' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +sanity_check_paths = { + 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', + 'lib/libcdt.%s' % SHLIB_EXT, 'lib/libgvc.%s' % SHLIB_EXT, 'lib/libxdot.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/graphviz'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/graphviz/python', + 'CLASSPATH': 'lib/graphviz/java/org/graphviz', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..fdd1e676cade3e5e1dbec20497004a4946843efc --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb @@ -0,0 +1,18 @@ +name = 'Gurobi' +version = '6.5.2' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# registration is required +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..758e95aed3dbbb4c3bb8f3db3f3ad288fbe8e88d --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb @@ -0,0 +1,18 @@ +name = 'Gurobi' +version = '7.0.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# registration is required +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb new file mode 100644 index 0000000000000000000000000000000000000000..18f71c6334b1e1d754aa26e157ea72c6066e8007 --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2016.08' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '4.9.4-2.25' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('CUDA', '7.5.18', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..ddfec681fb52b231f1fc44242ae73aab61a996ee --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2016.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('CUDA', '8.0.44', '', comp), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000000000000000000000000000000000..b799146d375484f2b879971e91c07cf0418ce015 --- /dev/null +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -0,0 +1,35 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'Conda' + +name = "gencore_variant_detection" +version = "1.0" +variant = "Linux-x86_64" + +homepage = "https://nyuad-cgsb.github.io/variant_detection/public/index.html" +description = """ This is a bundled install of many software packages for doing variant detection analysis. """ + +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' +remote_environment = "nyuad-cgsb/%(name)s_%(version)s" + +sanity_check_paths = { + 'files': ["bin/conda"], + 'dirs': [] +} + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000000000000000000000000000000000..991e6da6fa638df04d53a8dd92704859848cfbe1 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'gensim' +version = '0.13.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('requests', '2.10.0', '-Python-%(pyver)s'), +] + +exts_list = [ + ('boto', '2.42.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + }), + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + }), + ('smart_open', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/s/%(name)s'], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/%(name)s'], + }), +] + +# 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 = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..68b4d25ce93c13c77ac16c7e2d6e7ec7fb960f81 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +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 +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] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..ed81b95755a6bd661789a3d4b8c9c1677cf5cac1 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +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 +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] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb new file mode 100644 index 0000000000000000000000000000000000000000..ce355420b29f29b3cfcfc413c7426256fcaea34d --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +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 +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] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb new file mode 100644 index 0000000000000000000000000000000000000000..578b07b38d3251d0eb20e2cfa52bd80ec2fe0a1f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +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 +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-foss-2016.04.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..47b250264e4c3f0317e6231c0347043a8fac0904 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +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 +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016.04'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..45caa1fde85d1e18b31d28b2386916b21e0fb853 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +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 +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/gnuplot/gnuplot-5.0.5-intel-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1181859b405511603a9318d59c967ef0f0ef2d6f --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-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': 'intel', '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 new file mode 100644 index 0000000000000000000000000000000000000000..5eca4152c8a45e53da71501d0f648b277ce85fdf --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -0,0 +1,22 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.07' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, +including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.1.0' +binutilsver = '2.27' +gccbinver = '%s-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('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 new file mode 100644 index 0000000000000000000000000000000000000000..b4350de73ad72da9ac3456b0a0226cc696bca269 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -0,0 +1,20 @@ +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)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb new file mode 100644 index 0000000000000000000000000000000000000000..1afeb092c2bf2dbdf3c2ae384e53e9f1b60b873f --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2016.08' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '4.9.4-2.25' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, # part of gcccuda + ('CUDA', '7.5.18', '', comp), # part of gcccuda + ('OpenMPI', '1.10.3', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..39f562c6fb8fe6759082207565dec66fe2a8f262 --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2016.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, # part of gcccuda + ('CUDA', '8.0.44', '', comp), # part of gcccuda + ('OpenMPI', '2.0.1', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb new file mode 100644 index 0000000000000000000000000000000000000000..82819f4c5ea1d4157d5016e74e363042a87281a0 --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2016.08' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '4.9.4-2.25' +comp = (comp_name, comp_ver) + +# toolchain used to build goolfc dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc_ver = version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.0' +blas = '-%s-%s%s' % (blaslib, blasver, blassuff) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, # part of gompic + ('CUDA', '7.5.18', '', comp), # part of gompic + ('OpenMPI', '1.10.3', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ee5c6f69609ed922c5dd3c5eadcfba2ce97cc4f --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2016.10' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# toolchain used to build goolfc dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc_ver = version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' +blas = '-%s-%s%s' % (blaslib, blasver, blassuff) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, # part of gompic + ('CUDA', '8.0.44', '', comp), # part of gompic + ('OpenMPI', '2.0.1', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.5', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ada07243f898b60493dadc6813792c086fa5eaf --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b4e90a24ee03913bcf9b1b36c9cd3d19b1518ed5 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = "gperftools" +version = "2.5" + +homepage = 'http://github.com/gperftools/gperftools' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] + +builddependencies = [('Autotools', '20150215')] +dependencies = [('libunwind', '1.1')] + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fbae9a2a859bc3e37255d1c7abdc9168fcb176eb --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = "gperftools" +version = "2.5" + +homepage = 'http://github.com/gperftools/gperftools' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] + +dependencies = [('libunwind', '1.1')] + +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..365523c52998e494a6b5672a01328a9f4514889a --- /dev/null +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-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': 'intel', '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/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..236bb5545448449a73ccca73db2b926e55c34b57 --- /dev/null +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.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': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('Python', '3.5.2'), + ('Graphviz', '2.38.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f80a99e7110b9291a808ba648c1bfdd381b435a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +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': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..d61bff1fffd789c7cdb00cb0c96015e70d27258f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..e3d38f197654f2ec0c787beb3e47c442f0cc06bb --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..1cc3adf6f76998497e96e6998282bdea49ecd0e6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.17' +versionsuffix = '-serial' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..ded2abcfa1cc2230cd9d42bcc80bc29540835d76 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.17' +versionsuffix = '-serial' + +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': '2016b'} +toolchainopts = {'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..83a592d05a588218c56f54e2d151527b802378d5 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.4' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['50119a693929e240b072d79e69dc211e'] + +dependencies = [ + ('NGS', '1.2.5'), + ('ncbi-vdb', '2.7.0'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$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/HPCG/HPCG-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb index 06eaeceafd5d35c93701c11d4bc29b8a3146796b..cc1b32254880ae22e9fb3e31dd71051601de2e16 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb @@ -11,4 +11,6 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['https://software.sandia.gov/hpcg/downloads/'] sources = [SOURCELOWER_TAR_GZ] +runtest = True + moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb index 1d3f7c2d895a29909697c522f95d327487892da7..550fcae2be78ce38ce3ba8b09fa431a45a57ab61 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb @@ -11,4 +11,6 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['https://software.sandia.gov/hpcg/downloads/'] sources = [SOURCELOWER_TAR_GZ] +runtest = True + moduleclass = 'math' 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 new file mode 100644 index 0000000000000000000000000000000000000000..112d6aa6345556e239cb730d1c4073806e3eaa9f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb @@ -0,0 +1,18 @@ +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.""" + +toolchain = {'name': 'pomkl', 'version': '2016.09'} +toolchainopts = {'optarch': True, '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-foss-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..c44018425b1dbf270179e425446855c4505a5065 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.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': '2016.07'} +toolchainopts = {'optarch': True, '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-foss-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb new file mode 100644 index 0000000000000000000000000000000000000000..be4db4593ebbf63dbc96873a396af3027feb9a97 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.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': '2016.09'} +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 new file mode 100644 index 0000000000000000000000000000000000000000..d1430d0e3a6cc7780a53459c1cc9876dca5fe4da --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.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': 'goolfc', 'version': '2016.08'} +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-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..fff961832d9eb1f2bd5d0454e15202579d40fb56 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.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': 'goolfc', 'version': '2016.10'} +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-2017.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb new file mode 100644 index 0000000000000000000000000000000000000000..48447ddb2875e9466b5abb785b368f313cd8781b --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.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': '2017.00'} +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-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..64700f3b27967a0a985c9d2e5a91f970cb3ee3f6 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.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': '2017.01'} +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 new file mode 100644 index 0000000000000000000000000000000000000000..05f316bde4de14d79681c71a46aa7e516f2bae68 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.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': 'intelcuda', 'version': '2016.10'} +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..22cd32989a753684726798def06fc6c15b6b3f24 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.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': '2016.09-GCC-4.9.3-2.25'} +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..efda5a282ce5a5f4aa3691d405ea905127397b4a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.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': '2016.09-GCC-5.4.0-2.26'} +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-iomkl-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..d890354a7b87adf022e459e30c45d8348dae4f5a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.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': '2017.01'} +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 new file mode 100644 index 0000000000000000000000000000000000000000..005a57564c099d9d6127e09c08dd53386f3ab522 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.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': 'pomkl', 'version': '2016.09'} +toolchainopts = {'optarch': True, '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/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7f13d0e1c7e96714339f612dcd74c281e11ff63 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..12d319ea7b1d3562b30ccc55cfb2111ca3959d6f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HTSeq' +version = '0.6.1p1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +sanity_check_paths = { + 'files': ['bin/htseq-count', 'bin/htseq-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..71dc9972065b0a04f2f9ad28517c9bee99d2b948 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.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 +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + HTSlib also provides the bgzip, htsfile, and tabix utilities""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/htslib/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/htsfile", "bin/tabix", "include/htslib/hts.h", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..38ae993dca4aada59a02819f1f68f8750f303918 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.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 +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + HTSlib also provides the bgzip, htsfile, and tabix utilities""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/htslib/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/htsfile", "bin/tabix", "include/htslib/hts.h", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0528a8f0cc999c0654f4f172939e74108513ecd --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb @@ -0,0 +1,27 @@ +# 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 = 'HTSlib' +version = '1.3.2' + +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] + +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/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c081e2c8ed708fa18f5b135ab4d9fe38513a8eb --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.2.7' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('freetype', '2.6.3'), + ('GObject-Introspection', '1.48.0') +] + +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/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a9022cf44825085bba6e6a38f5411c9b570cae7 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-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': 'intel', '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/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb new file mode 100644 index 0000000000000000000000000000000000000000..156acadec823ec9f2b8dc83a875ecf643fc7d953 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +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] + +hdf5ver = '1.8.17' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.5.2'), + ('HDF5', hdf5ver), + ('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/hanythingondemand/hanythingondemand-3.1.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb new file mode 100644 index 0000000000000000000000000000000000000000..275b2940c7532bcfce2f2ca03605138b03cd6e07 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.4' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.1'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..f133f273c4776ca0274d63927f9db68dee6a7499 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.12'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb new file mode 100644 index 0000000000000000000000000000000000000000..7e255dbc21069de0b625f82f16495165f31314e6 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.0' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.1'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea99d52247b78ed9ead8f919a041e46d08e8fc97 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.12'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..53cf30b69c1b9d4b4e2ac8ad3db14e8e6bea72ff --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.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': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..659a1fdf2707136c18fe56ee61171ff2a815531e --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': '6.1.0-2.27'} + +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-1.11.3-gcccuda-2016.08.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb new file mode 100644 index 0000000000000000000000000000000000000000..4a821b0537ffef4981ea5eb08c4b92074d744ad6 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = "1.11.3" + +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': '2016.08'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..d786ed3e2f845934b0178d1b359c1d9d6cc261a6 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': '2016.3.210-GCC-4.9.3-2.25'} + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' 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 new file mode 100644 index 0000000000000000000000000000000000000000..35ced3699b49ed078f23acf88ef16609aca3680e --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb @@ -0,0 +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=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..6138766fd96125e0883568b510d809df507f32ab --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['b6f23eb59074fd09fdd84905d50b103d'] + +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '5.4.0')), +] + +configopts = "--enable-libnuma=$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 new file mode 100644 index 0000000000000000000000000000000000000000..a83862d85314b3221ef2ad6b80eaf180672990b3 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb @@ -0,0 +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=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..a68a5876d6c90bb9f4f1569e40d5a404d6c6becd --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['b6f23eb59074fd09fdd84905d50b103d'] + +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '5.4.0')), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..09fb675534c8273b75415b919951cb4fee09aa31 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -0,0 +1,30 @@ +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': '2016a'} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' +buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'dirs': ['bin','doc'] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 505c2f3911bcd7130d07a2b05c7695f57dfc1b69..2cca42e4db17e4f3fc75752f4d22c32041e161ea 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -1,40 +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 = 'Binary' +# authors: +# * Pablo Escobar Lopez (sciCORE - University of Basel - SIB Swiss Institute of Bioinformatics) +# * Benjamin Roberts (Landcare Research NZ Ltd) name = 'IMOD' version = '4.7.15' versionsuffix = '_RHEL6-64_CUDA6.0' homepage = 'http://bio3d.colorado.edu/imod/' -description = """IMOD is a set of image processing, modeling and display programs - used for tomographic reconstruction and for 3D reconstruction of EM serial sections - and optical sections.""" +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh'] -dependencies = [('Java', '1.7.0_80')] - -install_cmd = "csh %(namelower)s_%(version)s%(versionsuffix)s.csh -dir %(installdir)s -script %(installdir)s/ -yes" - -# the provied init script located in %(installdir)s also defines a bash/csh function named 'subm'. -# It's not possible to define a function in the module file -modloadmsg = """Bash users run: 'source $EBROOTIMOD/IMOD-linux.sh' -csh users run: 'source $EBROOTIMOD/IMOD-linux.csh'""" - -modextravars = { - 'IMOD_JAVADIR': '\$EBROOTJAVA', -} - -sanity_check_paths = { - 'files': ['IMOD/bin/imod'], - 'dirs': [], -} +dependencies = [ + ('CUDA', '6.0.37'), + ('Java', '1.7.0_80'), +] -moduleclass = 'bio' +moduleclass = 'vis' 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 b9a9c116d291d79b2a553625491e7d464b57d782..d3bbfe47b7c0bfcd1a26acaac76cee676caa0ccf 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 @@ -18,7 +18,9 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - ('entrypoints', '0.2.2', versionsuffix), + # required by 'nbconvert', but causes problems w.r.t. 'backports' module... + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -41,6 +43,7 @@ exts_list = [ }), ('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/'], @@ -60,6 +63,7 @@ exts_list = [ }), ('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/'], @@ -110,9 +114,11 @@ exts_list = [ ('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/'], - }), + # disabled because entrypoints on which this depends pull in configparser, which causes problems + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('nbconvert', '4.2.0', { + # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + #}), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), @@ -124,6 +130,12 @@ exts_list = [ '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']} diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f205e1577f2e058d6183b434061187ae2ab57651 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,142 @@ +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': 'intel', 'version': '2016b'} + +dependencies = [ + ('Python', '3.5.2'), + ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), + ('testpath', '0.3', 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/'], + }), + ('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/'], + }), + ('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/'], + }), + ('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', ''), + ('iptest3', ''), +] + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000000000000000000000000000000000..f3c4211e8402f81d9ec9f85e50cdb6e19b97cc76 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb @@ -0,0 +1,41 @@ +# 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 = '7.0.3-1' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20160819'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('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/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2388f280096784e9e0ffd1f05c1795bfef35d8e0 --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'InterProScan' +version = '5.21-60.0' + +homepage = 'http://www.ebi.ac.uk/interpro/' +description = """InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines + different protein signature recognition methods into one resource.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', + 'http://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/bin/', +] +sources = [ + '%(namelower)s-%(version)s-64-bit.tar.gz', + 'sfld_binary.zip', +] +checksums = [ + '8090ff00ba75bce1383a257ff2b8d196', + '17ff8224789b9f35dd9304dcb7dc6a68', +] + +dependencies = [ + ('Java', '1.7.0_80', '', True), + ('Perl', '5.20.3'), + ('libgd', '2.1.1'), + ('Python', '2.7.10'), +] + +# Workaround required for CentOS 6 systems. Details here: +# https://github.com/ebi-pf-team/interproscan/issues/16 +postinstallcmds = [ + "cp -f %(builddir)s/sfld_postprocess %(installdir)s/bin/sfld/", + "cp -f %(builddir)s/sfld_preprocess %(installdir)s/bin/sfld/", +] + +sanity_check_paths = { + 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], + 'dirs': ['bin', 'lib', 'data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0645a78ef1d8b11587018e659d43fc8b250dcff --- /dev/null +++ b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb @@ -0,0 +1,16 @@ +name = 'IronPython' +version = '2.7' + +homepage = 'http://ironpython.net/' +description = """IronPython is an open-source implementation of the Python programming language + which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and +Python libraries, and other .NET languages can use Python code just as easily.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/IronLanguages/main/archive/'] +sources = ['ipy-%(version)s.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lang' 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 5d57424030b47e665dedd5365de6e5f002aab098..efeb188af27eb851a0f7a33b1149ce3267a240f9 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 @@ -41,7 +41,7 @@ dependencies = [ ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), ('MySQL-python', '1.2.5', versionsuffix + '-MariaDB-10.1.14'), ('ImageMagick', '6.9.4-8'), - ('STAMP', '1.2'), + ('STAMP', '1.3'), ('Cluster-Buster', '20160106'), ('Kent_tools', '20130806', '-linux.x86_64', True), ] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1cc307109d8d9fe16605c02e80172767ae155e8 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2017.0.098' + +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_composer_edition_for_cpp.tgz'] + +checksums = ['c8a2fdb1501fbc93bfaad93195677d86'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..924f53625d1f2e171833d3f65778c94428572c30 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.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 = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ed3f947b9c1e37ef1ba5888c177bb2babe2fb96 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +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""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000000000000000000000000000000000..8034a2a1e14089ff5211cca11129875e8239d2e7 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2017.1.132' +versionsuffix = '-GCC-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""" + +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 new file mode 100644 index 0000000000000000000000000000000000000000..1eeb749c6e9c13c431085f724270ac234986473e --- /dev/null +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +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""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'iccifort' +comp_ver = '2016.3.210' +gccver = '5.4.0' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +cudacomp = (comp_name, '%s%s' % (comp_ver, gccsuff)) + +dependencies = [ + ('icc', comp_ver, gccsuff), + ('ifort', comp_ver, gccsuff), + ('CUDA', '8.0.44', '', cudacomp), +] + +moduleclass = 'toolchain' 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 d331cd8e4a550d99529d4e4a37f49a48f78c78c8..9599d683487fc263f0e6d899ea6c977513b6ba29 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 @@ -4,12 +4,15 @@ name = 'ifort' version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + checksums = ['bce7f6a71f7e44f67956197501d00b7c'] gccver = '4.9.3' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index c64470205a7a7123fbab6c4b14f5a796823c83ad..657a607db362a9a50db4d18b83f05958d563fc18 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + # 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 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 aee6ae915ef9191c408fb4fd85bf073126ccaf67..9afeb8bcc99b8c6a5523c76af2fb6b32097b9c55 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 @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': ''} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['1e848c8283cf6a0210bce1d35ecd748b'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '4.9.3' binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index ffe995c4ac47d86db8e0533cf7a81485c97c4801..39dd0065521f55fc7270cb627d3a361d5ab453e3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '4.9.3' binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 5844c8abd9ac08bf0718250d6390280218d0942d..952e908d84556dc86f4af220772b86e73d0cb795 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '5.3.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 303793bfad7bc581285dddee4f2c82ef66528300..624fe2510b746c9199980ba641824cb14e265159 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '4.9.3' binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index b354753609298ae005d9a9487b713c908a940db3..148dc067648ae426e022a4bef20434cf1c0e9931 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '5.3.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 29953965f2869faaf89aff44b8831e06a5f00840..48e857188b4bdaab9adc156fcbc2e41010ca889d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Fortran compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '5.4.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..26de8ad2549f7fe4b22ea1304313e1624ddd0f5e --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2017.0.098' + +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_composer_edition_for_fortran.tgz'] + +checksums = ['8787795951fe10f90ce7dcdcec1b9341'] + +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..c275933f9dd128a6b33947d0cdc2b91dc02f69b6 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.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 = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch b/easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch new file mode 100644 index 0000000000000000000000000000000000000000..6c852c220dc0f5ab340e1051e6a762c3ecdd9fa9 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch @@ -0,0 +1,13 @@ +Eliminate dependency on intel-mpi-rt-mic which in turn brings in intel-mpi-rt. +author: Bart Oldeman (McGill HPC) +--- pset/mediaconfig.xml.orig 2016-11-14 12:57:14.214649000 -0500 ++++ pset/mediaconfig.xml 2016-11-14 12:57:30.108947210 -0500 +@@ -1758,7 +1758,7 @@ + ${PACKAGE_DIR}/rpm + rpm + +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel(R) Fortran Compiler 16.0 Update 2 + インテル(R) Fortran コンパイラー (インテル(R) 64) diff --git a/easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch b/easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch new file mode 100644 index 0000000000000000000000000000000000000000..8d3929a0f53c8cb9af34feb96fc241905fb8c121 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch @@ -0,0 +1,13 @@ +Eliminate dependency on intel-mpi-rt-mic which in turn brings in intel-mpi-rt. +author: Bart Oldeman (McGill HPC) +--- pset/mediaconfig.xml.orig 2016-10-20 09:02:57.000000000 +0000 ++++ pset/mediaconfig.xml 2016-11-11 20:09:08.084892189 +0000 +@@ -1551,7 +1551,7 @@ + ${BUNDLE_MAPFILE_DIR} + ${BUNDLE_CHKLIC_IA32} + +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel(R) Fortran Compiler 17.0 Update 1 + インテル(R) Fortran コンパイラー (インテル(R) 64) diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..1af95a3473e8e410a77be258fa04eef239dd3c89 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017.00' +versionsuffix = '-GCC-5.4.0-2.26' + +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 = '2017.0.098' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '2017.0.098', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..97332c6ea3808843f5b35431d8ce1c3f37bd00ea --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017.01' +versionsuffix = '-GCC-5.4.0-2.26' + +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' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..33bf002bbfa5e3486c3a4c7406dd3700f76794e1 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb @@ -0,0 +1,23 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpic' +version = '2016.10' + +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 = '2016.3.210' +suff = '-GCC-5.4.0-2.26' +comp = ('iccifort', '%s%s' % (compver, suff)) + +dependencies = [ + ('icc', compver, suff), + ('ifort', compver, suff), + ('CUDA', '8.0.44', '', comp), + ('impi', '5.1.3.181', '', ('iccifortcuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb deleted file mode 100644 index 4d5ef42fcf1ae19862198e6890807257f9e08ad7..0000000000000000000000000000000000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'imkl' -version = '10.3.12.361' - -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': 'dummy', 'version': ''} - -sources = ['l_mkl_%(version)s.tgz'] - -compver = '2011.13.367' -comp = ('iccifort', compver) - -# deps for interface build -mpi = 'MVAPICH2' -mpiver = '1.9' -versionsuffix = '-%s-%s' % (mpi, mpiver) - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (mpi, mpiver, '', comp), -] - -dontcreateinstalldir = 'True' - -interfaces = True - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb deleted file mode 100644 index 2bd88ac625c46afa75b23783cd16177323c9645e..0000000000000000000000000000000000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'imkl' -version = '10.3.12.361' - -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': 'dummy', 'version': ''} - -sources = ['l_mkl_%(version)s.tgz'] - -compver = '2011.13.367' -comp = ('iccifort', compver) - -# deps for interface build -mpi = 'OpenMPI' -mpiver = '1.6.3' -versionsuffix = '-%s-%s' % (mpi, mpiver) - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (mpi, mpiver, '', comp), -] - -dontcreateinstalldir = 'True' - -interfaces = True - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..601460577a3543f1b7ebdf4f7fb7f738a1372103 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +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': 'iimpic', 'version': '2016.10'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.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.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..bbbfc083fb7ace6586906892fb3ec05aac751100 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +name = 'imkl' +version = '11.3.3.210' + +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': '2016.09-GCC-4.9.3-2.25'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +interfaces = True + +license_file = HOME + '/licenses/intel/license.lic' + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.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.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..4739cbc29056ea33463d6a40e0a56a78087354e0 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb @@ -0,0 +1,36 @@ +name = 'imkl' +version = '11.3.3.210' + +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': '2016.09-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +interfaces = True + +license_file = HOME + '/licenses/intel/license.lic' + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.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.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea94f4aa6a31332cbfb3b95257e90af0538394ee --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +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': 'pompi', 'version': '2016.09'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +components = ['intel-mkl'] + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.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.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..341dbab7ed44ce75dbc27cd404ced266444ce737 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.0.098' + +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': '2017.00-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['3cdcb739ab5ab1e047eb130b9ffdd8d0'] + +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-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..be8b68226a4ec99740c780d6ca7ef33bd9bdcbf3 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.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': '2017.01-GCC-5.4.0-2.26'} + +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-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f68711972415194cddb5f1e188ffe990fdde403 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.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': '2017.01'} + +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/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..867202a35792cdba6f8cdb01fc904197e4cf507d --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '2017.0.098' + +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': '2017.0.098-GCC-5.4.0-2.26'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['fc123875773816b7084a91e419d54d20'] + +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-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..bebecd8cf61eca7ead1fe486b10f8cc097a5bc87 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.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-5.4.0-2.26'} + +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-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..292b8c704ec50e0ee9b6468c87fe3a124b9aa947 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +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': 'iccifortcuda', 'version': '2016.10'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.00.eb b/easybuild/easyconfigs/i/intel/intel-2017.00.eb new file mode 100644 index 0000000000000000000000000000000000000000..ad8be63148a87d6eb827c77331cc04190cc877eb --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.00.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +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.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.0.098' +gccver = '5.4.0' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '2017.0.098', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '2017.0.098', '', ('iimpi', version + gccsuff)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.01.eb b/easybuild/easyconfigs/i/intel/intel-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..9993bc8e4708c7117307c5cb060e8c3d0dd63298 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.01.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +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.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +gccver = '5.4.0' +binutilsver = '2.26' +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/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..ac6a734e6e5e2ca6335058c415243be07c7e3f9a --- /dev/null +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +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""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'iccifort' +comp_ver = '2016.3.210' +gccver = '5.4.0' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +comp = (comp_name, '%s%s' % (comp_ver, gccsuff)) + +dependencies = [ + comp, # part of iimpic + ('CUDA', '8.0.44', '', comp), + ('icc', comp_ver, gccsuff), + ('ifort', comp_ver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifortcuda', version)), + ('imkl', '11.3.3.210', '', ('iimpic', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..c5a095b3f6afe8ef802835ee1c92a1bdf27796be --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.24.0' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44_01', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..cf9954cf88316acdf02c8c9abff7b7dce5e4958d --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +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.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210-GCC-4.9.3-2.25' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.10.4', '', ('iccifort', compver)), + ('imkl', '11.3.3.210', '', ('iompi', version)), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000000000000000000000000000000000..6b0377e8e38cfad4db53a54c3c390e39f4bb08dc --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +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.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210-GCC-5.4.0-2.26' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), + ('imkl', '11.3.3.210', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..6039ebaad32a322be08743588d0db8eaf6b63ddb --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +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.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +gcc_maj_min = '5.4' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('OpenMPI', '2.0.1', '', ('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 new file mode 100644 index 0000000000000000000000000000000000000000..3c9854b3e19ce4561dad5987d8fecc449e974c9b --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2016.09-GCC-4.9.3-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210-GCC-4.9.3-2.25' + +dependencies = [ + ('OpenMPI', '1.10.4', '', ('iccifort', compver)), + ('icc', compver), + ('ifort', compver), +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..6ab1a7b7d5b8f606aa521a0e2e8f78eb664b81de --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2016.09-GCC-5.4.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210-GCC-5.4.0-2.26' + +dependencies = [ + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), + ('icc', compver), + ('ifort', compver), +] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c2c6b52a508a319a390ae535be556f7fe6b0dd4 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb @@ -0,0 +1,21 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iompi' +version = '2017.01' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +compversuff = '-GCC-5.4.0-2.26' + +dependencies = [ + ('icc', compver, compversuff), + ('ifort', compver, compversuff), + ('OpenMPI', '2.0.1', '', ('iccifort', '%s%s' % (compver, compversuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec1642238fe539e6888236328c7128215e7aa0b4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.6.0_24' + +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.bin' % altver] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b87f36815bcb59f5285a0bd85a3eb37bde0401f --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_112' + +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 new file mode 100644 index 0000000000000000000000000000000000000000..00bc8cb97d9e349ff8551f3b206b12658f6e9ec4 --- /dev/null +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.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 + +easyblock = 'PackedBinary' + +name = 'jModelTest' +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.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('ant', '1.9.7', versionsuffix)] + +dependencies = [ + ('MPJ-Express', '0.44', versionsuffix, ('foss', '2016a')), + ('Java', '1.8.0_92'), +] + +install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" + +modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" + +sanity_check_paths = { + 'files': ['jModelTest.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7ab95453f84c67f59745e50fabb07d306598c102 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.2.1' + +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': '2016b'} + +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/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..418b1b87b0efcc1bb7fcb67c139b8759bf100001 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Keras' +version = '1.0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('Theano', '0.8.2', versionsuffix), + ('h5py', '2.6.0', '%(versionsuffix)s-HDF5-1.8.17'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..503271be943e0bf503f3eb768410b1e1d633c509 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Keras' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('Theano', '0.8.2', versionsuffix), + ('h5py', '2.6.0', '%(versionsuffix)s-HDF5-1.8.17'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..68addbe81706d6001f8a410ccd5e845f1deb0a48 --- /dev/null +++ b/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.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 +# 1.4.1 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'khmer' +version = '1.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ged-lab/khmer/' +description = """ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ged-lab/khmer/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["count-median.py", "extract-long-sequences.py", "filter-abund.py", + "load-into-counting.py", "sample-reads-randomly.py"]], + 'dirs': ["lib/python%(pyshortver)s/site-packages/khmer-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7a88ce495d30a705dfbcc9e541915c8be8ce408 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb @@ -0,0 +1,46 @@ +# 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 = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' + +description = """LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to + handle sequences the size of human chromosomes and from different species, it is also useful for sequences + produced by NGS sequencing technologies such as Roche 454.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +# the tarball includes some test data which is not copied when doing the "make install" step. +# We use the buildininstalldir option to keep this test data in the %(installdir)s +buildininstalldir = True + +parallel = 1 + +unpack_options = '--strip-components=1' + +skipsteps = ['configure'] + +# by default definedForAll variable in src/Makefile contains -Werror which works with gcc-4.4 +# but crashes with newer gcc versions so we override definedForAll to remove the -Werror option +buildopts = " definedForAll='-Wall -Wextra -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE'" + +# use the LASTZ_INSTALL variable to define the directory where to copy the binaries during "make install" step +# Tarball includes an empty bin/ folder. In case the tarball doesn't include a bin/ folder you can do +# preinstallopts = 'mkdir %(installdir)s/bin/ && ' +installopts = " LASTZ_INSTALL='%(installdir)s/bin'" + +sanity_check_paths = { + 'files': ["bin/lastz", "bin/lastz_D"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a5106af44b13e3ccb0592a79744cc0130554ee6 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.9.0' + +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': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +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/LLVM/LLVM-3.9.0-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2bf426d402314b9f516138fab8fa46fe2ca7ef52 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.9.0' + +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': '2016b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +patches = ['LLVM-3.9.0-intel-fix-loop.patch'] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +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 ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +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/LLVM/LLVM-3.9.0-intel-fix-loop.patch b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-fix-loop.patch new file mode 100644 index 0000000000000000000000000000000000000000..33e6578be43522e81d3c090af4cb8f72603db1f3 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-fix-loop.patch @@ -0,0 +1,26 @@ +# Bug in intel compiler +# Source: From https://sft.its.cern.ch/jira/browse/ROOT-8233 +diff -ur llvm-3.9.0rc3.src.orig/lib/Transforms/Utils/LoopUtils.cpp llvm-3.9.0rc3.src/lib/Transforms/Utils/LoopUtils.cpp +--- llvm-3.9.0rc3.src.orig/lib/Transforms/Utils/LoopUtils.cpp 2016-06-11 23:48:25.000000000 +0200 ++++ llvm-3.9.0rc3.src/lib/Transforms/Utils/LoopUtils.cpp 2016-09-01 11:40:34.394205219 +0200 +@@ -834,6 +834,11 @@ + return UsedOutside; + } + ++namespace llvm { ++ extern char &LoopSimplifyID; ++ extern char &LCSSAID; ++} ++ + void llvm::getLoopAnalysisUsage(AnalysisUsage &AU) { + // By definition, all loop passes need the LoopInfo analysis and the + // Dominator tree it depends on. Because they all participate in the loop +@@ -845,8 +850,6 @@ + + // We must also preserve LoopSimplify and LCSSA. We locally access their IDs + // here because users shouldn't directly get them from this header. +- extern char &LoopSimplifyID; +- extern char &LCSSAID; + AU.addRequiredID(LoopSimplifyID); + AU.addPreservedID(LoopSimplifyID); + AU.addRequiredID(LCSSAID); diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6e7ff8a59616911358f279418b32a22124067281 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-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 +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.09' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "LZO-2.06: Portable lossless data compression library" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage + 'download/'] + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..128c5bbc07bbdc51f814b4bbeea20e5d339881b0 --- /dev/null +++ b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'LeadIT' +version = '2.1.9' + +homepage = 'http://www.biosolveit.de/LeadIT/index.html' +description = """Visually Informed LeadOpt""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +#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'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["leadit", "flexv", "hydescorer"], + 'dirs': ["example", "doc"] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8282cb93ccd351b27d73c0799d7beae40ee1bd18 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb @@ -0,0 +1,21 @@ +name = 'Libint' +version = '2.1.0' + +homepage = 'https://github.com/evaleev/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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['https://github.com/evaleev/libint/releases/download/v%(version)s'] + +builddependencies = [ + ('GMP', '6.1.1'), + ('Boost', '1.61.0', '-Python-2.7.12'), + ('Eigen', '3.2.9'), + ('Python', '2.7.12'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..738095618f9ca021e29a25ebab1382e5d5e14330 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.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': '2016b'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.5.0')] + +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/LoFreq/LoFreq-2.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..e9aae8deda622e3dd5a8a755e154d8cfade08f94 --- /dev/null +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'LoFreq' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://csb5.github.io/lofreq' +description = "Fast and sensitive variant calling from next-gen sequencing data" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lofreq_star-%(version)s.tar.gz'] + +patches = ['LoFreq-%(version)s_SAMtools-HTSlib.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('SAMtools', '1.3.1', '-HTSlib-1.3.2'), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/lofreq'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('python', "-c 'import lofreq_star'")] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.2_SAMtools-HTSlib.patch b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.2_SAMtools-HTSlib.patch new file mode 100644 index 0000000000000000000000000000000000000000..2ea3e4a060b70c57cd4a5badf8a315157dacb442 --- /dev/null +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.2_SAMtools-HTSlib.patch @@ -0,0 +1,126 @@ +patch out hard requirement for SAMtools and HTSlib locations that provides sources, there's no reason at all for it, +and link to SAMtools and HTSlib libraries provided through EasyBuild instead; +undefine bam_nt16_nt4_table symbol to dance around https://github.com/CSB5/lofreq/issues/28 +author: Kenneth Hoste (HPC-UGent) +diff -ur lofreq_star-2.1.2.orig/configure lofreq_star-2.1.2/configure +--- lofreq_star-2.1.2.orig/configure 2015-05-19 07:40:54.000000000 +0200 ++++ lofreq_star-2.1.2/configure 2016-11-22 11:10:50.084224167 +0100 +@@ -14376,78 +14376,6 @@ + #AC_LIB_LINKFLAGS([hts]) + #AC_LIB_LINKFLAGS([bam]) + +-if test x"$SAMTOOLS" = x""; then +- { { $as_echo "$as_me:$LINENO: error: Samtools directory not defined. Please use SAMTOOLS=/fullpath/to/samtoolsdir/" >&5 +-$as_echo "$as_me: error: Samtools directory not defined. Please use SAMTOOLS=/fullpath/to/samtoolsdir/" >&2;} +- { (exit 1); exit 1; }; } +-fi +- +-if test x"$HTSLIB" = x""; then +- { { $as_echo "$as_me:$LINENO: error: Htslib directory not defined. Please use HTSLIB=/fullpath/to/htslibdir/" >&5 +-$as_echo "$as_me: error: Htslib directory not defined. Please use HTSLIB=/fullpath/to/htslibdir/" >&2;} +- { (exit 1); exit 1; }; } +-fi +-as_ac_File=`$as_echo "ac_cv_file_${SAMTOOLS}/bam.h" | $as_tr_sh` +-{ $as_echo "$as_me:$LINENO: checking for ${SAMTOOLS}/bam.h" >&5 +-$as_echo_n "checking for ${SAMTOOLS}/bam.h... " >&6; } +-if { as_var=$as_ac_File; eval "test \"\${$as_var+set}\" = set"; }; then +- $as_echo_n "(cached) " >&6 +-else +- test "$cross_compiling" = yes && +- { { $as_echo "$as_me:$LINENO: error: cannot check for file existence when cross compiling" >&5 +-$as_echo "$as_me: error: cannot check for file existence when cross compiling" >&2;} +- { (exit 1); exit 1; }; } +-if test -r "${SAMTOOLS}/bam.h"; then +- eval "$as_ac_File=yes" +-else +- eval "$as_ac_File=no" +-fi +-fi +-ac_res=`eval 'as_val=${'$as_ac_File'} +- $as_echo "$as_val"'` +- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +-$as_echo "$ac_res" >&6; } +-as_val=`eval 'as_val=${'$as_ac_File'} +- $as_echo "$as_val"'` +- if test "x$as_val" = x""yes; then +- : +-else +- { { $as_echo "$as_me:$LINENO: error: bam.h not found" >&5 +-$as_echo "$as_me: error: bam.h not found" >&2;} +- { (exit 1); exit 1; }; } +-fi +- +-as_ac_File=`$as_echo "ac_cv_file_${HTSLIB}/htslib/hts.h" | $as_tr_sh` +-{ $as_echo "$as_me:$LINENO: checking for ${HTSLIB}/htslib/hts.h" >&5 +-$as_echo_n "checking for ${HTSLIB}/htslib/hts.h... " >&6; } +-if { as_var=$as_ac_File; eval "test \"\${$as_var+set}\" = set"; }; then +- $as_echo_n "(cached) " >&6 +-else +- test "$cross_compiling" = yes && +- { { $as_echo "$as_me:$LINENO: error: cannot check for file existence when cross compiling" >&5 +-$as_echo "$as_me: error: cannot check for file existence when cross compiling" >&2;} +- { (exit 1); exit 1; }; } +-if test -r "${HTSLIB}/htslib/hts.h"; then +- eval "$as_ac_File=yes" +-else +- eval "$as_ac_File=no" +-fi +-fi +-ac_res=`eval 'as_val=${'$as_ac_File'} +- $as_echo "$as_val"'` +- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +-$as_echo "$ac_res" >&6; } +-as_val=`eval 'as_val=${'$as_ac_File'} +- $as_echo "$as_val"'` +- if test "x$as_val" = x""yes; then +- : +-else +- { { $as_echo "$as_me:$LINENO: error: hts.h not found" >&5 +-$as_echo "$as_me: error: hts.h not found" >&2;} +- { (exit 1); exit 1; }; } +-fi +- +- + + + +diff -ur lofreq_star-2.1.2.orig/src/lofreq/Makefile.in lofreq_star-2.1.2/src/lofreq/Makefile.in +--- lofreq_star-2.1.2.orig/src/lofreq/Makefile.in 2015-05-19 07:40:55.000000000 +0200 ++++ lofreq_star-2.1.2/src/lofreq/Makefile.in 2016-11-22 11:10:52.064187293 +0100 +@@ -58,7 +58,7 @@ + samutils.$(OBJEXT) snpcaller.$(OBJEXT) utils.$(OBJEXT) \ + vcf.$(OBJEXT) viterbi.$(OBJEXT) + lofreq_OBJECTS = $(am_lofreq_OBJECTS) +-lofreq_DEPENDENCIES = @HTSLIB@/libhts.a @SAMTOOLS@/libbam.a \ ++lofreq_DEPENDENCIES = $(EBROOTHTSLIB)/lib/libhts.a $(EBROOTSAMTOOLS)/lib/libbam.a \ + ../cdflib90/libcdf.a + DEFAULT_INCLUDES = -I.@am__isrc@ + depcomp = $(SHELL) $(top_srcdir)/depcomp +@@ -80,7 +80,7 @@ + DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) + ACLOCAL = @ACLOCAL@ + AMTAR = @AMTAR@ +-AM_CFLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../cdflib90/ -I../uthash -I@HTSLIB@ -I@SAMTOOLS@ @AM_CFLAGS@ ++AM_CFLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../cdflib90/ -I../uthash -I$(EBROOTHTSLIB)/include -I$(EBROOTSAMTOOLS)/include/bam @AM_CFLAGS@ + AM_LDFLAGS = @AM_LDFLAGS@ + AR = @AR@ + AUTOCONF = @AUTOCONF@ +@@ -234,7 +234,7 @@ + + # note: order matters + #lofreq_LDADD = @htslib_dir@/libhts.a @samtools_dir@/libbam.a +-lofreq_LDADD = @HTSLIB@/libhts.a @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a ++lofreq_LDADD = $(EBROOTHTSLIB)/lib/libhts.a $(EBROOTSAMTOOLS)/lib/libbam.a ../cdflib90/libcdf.a + all: all-am + + .SUFFIXES: + +--- lofreq_star-2.1.2.orig/src/lofreq/bam_md_ext.h 2016-11-22 12:36:36.740198311 +0100 ++++ lofreq_star-2.1.2/src/lofreq/bam_md_ext.h 2016-11-22 12:36:46.820255151 +0100 +@@ -31,4 +31,6 @@ + int baq_flag, int ext_baq, int idaq_flag); + + ++#undef bam_nt16_nt4_table ++ + #endif diff --git a/easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb b/easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..da1c7223b7d6db420d0752847841fbb13a410e57 --- /dev/null +++ b/easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'PerlModule' + +name = 'Log-Log4perl' +version = '1.47' + +homepage = 'https://metacpan.org/pod/Log::Log4perl' +description = """Log4perl""" + +toolchain = {'name': 'foss', 'version': '2016a'} +source_urls = ['https://cpan.metacpan.org/authors/id/M/MS/MSCHILLI/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.22.1' +perlversuffix = '-bare' + +dependencies = [ + (perl, perlver, perlversuffix) +] + +options = {'modulename': 'Log::Log4perl'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb index b4e0ad7225ca00b35f7f007f787ae11aad3fc803..08d864aaf628672e6e666a6ae398fcc2944abb49 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -16,7 +16,13 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] -dependencies = [('ncurses', '6.0')] +builddependencies = [ + ('ncurses', '6.0'), + ('libreadline', '6.3') +] + +# Use static linking for ncurses so it's not a runtime dep +configopts = "--with-static=yes" sanity_check_paths = { 'files': ["bin/lua"], diff --git a/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..5abfa7b4da3d5ecf8b1d05f87b2a8e177d34ed80 --- /dev/null +++ b/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb @@ -0,0 +1,27 @@ +# 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 = 'lbzip2' +version = '2.5' + +homepage = 'http://lbzip2.org/' +description = """lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True} + +source_urls = ['http://archive.lbzip2.org/'] +sources = [SOURCELOWER_TAR_GZ] + +buildopts = ' check' + +sanity_check_paths = { + 'files': ['bin/lbunzip2', 'bin/lbzcat', 'bin/lbzip2'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..361489070d9e258967fff258f292c9700fd00dd4 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '12.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..51bb338e1e3a08c06dcd718f3673a7c69112ff33 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '12.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016b.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4edf05a0d20b30b5b0092c2fe1e940675e25b63d --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-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': '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/libcerf/libcerf-1.5-intel-2016b.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0cce9f8c9873b35f1d4af6a82e5e6a9341f9161c --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-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': 'intel', '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/libdrm/libdrm-2.4.70-foss-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d9e8ac938590bffa90d210a8b88e35cd512cd1b --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.70' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016b'} + +dependencies = [ + ('X11', '20160819'), +] + +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/libdrm/libdrm-2.4.70-intel-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9fb07a29545f25170359aec3e2d36abbfec691d0 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.70' + +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': '2016b'} + +dependencies = [ + ('X11', '20160819'), +] + +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/libffi/libffi-3.2.1-foss-2016.04.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..37b990fbd320e13c4d37e02ef55f68c618eab588 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016.04.eb @@ -0,0 +1,23 @@ +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': 'foss', 'version': '2016.04'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +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-intel-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..3a99421ffa1f3b4c87ef6d7018bcee9abbed4418 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-intel-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': 'intel', '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/libgtextutils/libgtextutils-0.7-foss-2016b.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c761422aa9981fcbcd242a045a25e04b473e997 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016b.eb @@ -0,0 +1,35 @@ +## +# 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 +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.7' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/libgtextutils/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..d619aa0f828733b0626c44ebe636cd1722452ba3 --- /dev/null +++ b/easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libibmad' +version = '1.3.12' + +homepage = 'http://www.openfabrics.org' +description = """libibmad is a convenience library to encode, decode, and dump IB MAD packets. It + is implemented on top of and in conjunction with libibumad (the umad kernel + interface library.)""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.openfabrics.org/downloads/management/'] + +dependencies = [('libibumad', '1.3.10.2')] + +sanity_check_paths = { + 'files': ['include/infiniband/mad.h', 'include/infiniband/mad_osd.h', + 'lib/libibmad.a', 'lib/libibmad.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..c2063cef0d60e2495ea213140131072c42624ff0 --- /dev/null +++ b/easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libibumad' +version = '1.3.10.2' + +homepage = 'http://www.openfabrics.org' +description = """libibumad is the umad kernel interface library.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.openfabrics.org/downloads/management/'] + +sanity_check_paths = { + 'files': ['include/infiniband/umad.h', 'lib/libibumad.a', 'lib/libibumad.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..8728627d19aae25f2dc4f6934455f062ff538971 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +nasmver = '2.12.01' +versionsuffix = '-NASM-%s' % nasmver + +dependencies = [ + ('NASM', nasmver), +] + +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/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5e74640f5a575b91c3784c931a5774147ffd5c2 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +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/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ecf772ccf16697ea7774b1b1d17ad8ed16ff38f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.12.02'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f690e65b23ce08b7a4c589a3e99abae68c11dfb --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.24' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', '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-1.6.26-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..83dd651c2b45b5c125facd4bb48561e32ca8ba17 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.26' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', '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-1.6.26-intel-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba71624bd16b8c3dcc02b0c2856bb6f353f1bac3 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.26' + +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/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 55d005e4b82e316d63398755953eb6f1d33547be..3d2321bd0603b3ed1715fa3f824cd4fce290eac1 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -10,6 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..25cb143653dd8483a339cc9d7e75ecad27980eec --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb @@ -0,0 +1,32 @@ +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': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '5.9')] + +# 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-6.3-foss-2016.04.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..14fbd4b55ee8f62ea7bd6af73167599c0c965599 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016.04.eb @@ -0,0 +1,32 @@ +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +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-6.3-iomkl-2016.07.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..8aff248e5213f7ab65b7540e888ce6d763da11b7 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.07.eb @@ -0,0 +1,32 @@ +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +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-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..04b53926ef82cec13045deaf53008cc4ede9587c --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +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-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..36625b171750d5840cf2356e929f32d1dd03f72a --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -0,0 +1,32 @@ +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': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +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/libtool/libtool-2.4.6-foss-2016.04.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..bc63db0c69cfa5eefd89f05d9d6bc87897149e57 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016.04.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': '2016.04'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..32d19e0439c04b301eb957fa768080d35ca1293f --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.07.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..436ada208a6d4b2da278fa333a0aaf3d564e0863 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..8730994eeb18a41db3a2e086c26d46bc2dec16f7 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..aea3c64e514e8e1c8a0f6ea4a2e611552eca3b4c --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..25e24ba97f44a5640db770f63302b6025539641c --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb @@ -0,0 +1,20 @@ +name = 'libxml2' +version = '2.9.2' + +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': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb index 6000926382854096d1c45abbe127984c1de72588..798eea2998235307d5d00aea8af3c0fb879a244b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb @@ -14,6 +14,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb index 6e41adde06a7d8fad73b733004d3b598e2360cc0..4873fafcda4f4fe7a885b55a2163ad7a73e521c1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb @@ -21,6 +21,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.8'), + ('XZ', '5.2.2'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..9268fd68be0c71eb527a9d7ed3c32a0301257608 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb @@ -0,0 +1,23 @@ +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb index e6cae216953f51c41ef4608786b6885a997ce090..59cbe77a84c29e822094e4106f30403a5a38f533 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..a047fc32c8cf8fb2f6569bebeb7c63762679dc9e --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), + ('Python', '2.7.12'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb index 09ede640fb9318ed5070c765e993b2c366cbf350..abee889e32e45347aeb79b9ea097e43f8db010fd 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f9093db10dc5a24283163bb309d0f081f838604 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), + ('Python', '2.7.12'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb index b41d38c5455e09fdd1fc86a75e63bc96b03316b2..ab1c0ecd3e4e06b1de1d0d901c284ae53423efa1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..ac1786bdfdaa83d8712748eff7c0fd4156c17f73 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +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': 'goolf', 'version': '1.5.16'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/', +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..af8ebb2524c8c5c363a1df7285b0d97283da57bd --- /dev/null +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'log4cplus' +version = '1.0.4.3' + +homepage = 'http://sourceforge.net/p/log4cplus' +description = """log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily +granular control over log management and configuration. It is modelled after the Java log4j API.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], + 'dirs': ["include/log4cplus"], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..bdb9d13739691ae9b476a9632c3188e684bfc9ab --- /dev/null +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'log4cplus' +version = '1.1.2' + +homepage = 'http://sourceforge.net/p/log4cplus' +description = """log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily +granular control over log management and configuration. It is modelled after the Java log4j API.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], + 'dirs': ["include/log4cplus"], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 8398e40d0665ca4cb92593c45b2d9755f0ab75a4..54365e5c1206734c1a95a0464750c447ee525c7f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index b84761b60206ddb7270a05110e8911573dff7510..41431f6ed6c5484a3c5bdee505d356dce83c7f57 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index b4bb4c955de91f15c5df15b89d700e7f478985b8..91d64e5bd3ca463f8b344a57f8c80f6eebe37200 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index 5df1dda5a3a107ec921112511cac14152963ffbc..cb0daa392fed324ffc6f1ae14f6baf34f4705b1b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index f406268a87d92714529bd138dc1bc61b06b4e56e..e59131c48fb164f143c5ad1fc8e82fdd9b62cc88 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index 560606e07ad3dd4ea3ca3539d3d9ad54d2b81db4..c9b8ae162c44b08a1ac4929fea3e223101785aa4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index 00b1eb05a83cdc8d243782bd6c3d2a161cfce06a..d52dd469f6af1dba71334ed29fc57a750fe82e60 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index a939e01023030f76edf9fecb7f56645dec2f7402..5658dda837723f361f5fcdb38eb782bcaf1fdecf 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 64c98aad337a5a17e87cac3f43c2d6d53179804d..006446b9f08e0bdb07bd4b5e70999a9c17ac94eb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index 745063ebad907909453d1dbb099e4b281055023e..e7a4d305fe1162d1b886824372d4ec88b8544f68 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index a95ac9f601f6972c311353e9c0e715fd747174cb..6e2de92ed5905e500ecaf1fd8622971719e3f5cb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb index 747a5dbe94e43b2e668fa1c142a4addeab38085b..ab6365038384b116ad80f0d641dd1fda0c4ab45d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb @@ -13,7 +13,9 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +# '-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"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb index 5551b81d856ade255716f92fadf4c88d12171249..4a7f47d9bcb40821121d9aa9cc78f32d3b32f4e9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index 02f06d5cfecef51fae9e7c29c4c0af3ff45ad090..72fbf1541bfd0865ca471fbb3a5243c0e67b9880 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb index fa161623a1fdccd55d977503dceedc9b3f898973..83effb6682bc6daab9c4a5d934fc9d58748617a2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index 434b6f02ff3f4b9dad73a58e0c12d4f92a307b03..d508b59ac77db2845ffda78be95c36b0d4987aaa 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -16,7 +16,9 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] -configopts = "--enable-cxx" +# '-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"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb index 114b490972e5c12a1a94a3850b8c331c2a6236d8..702e8595184d52126dd9f26b583214f6a082cd6e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -16,7 +16,9 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] -configopts = "--enable-cxx" +# '-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"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..87ca206fb45ee4783f0df54e6767cd8e2a59c466 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +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': '6.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCCcore +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/M4-1.4.17-GCCcore-6.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 6f774b05e4bfda54a86a927fb7ff49ee8fede310..9a89ad1fbdf638acdb27a35a66649bcbde50dd13 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -16,7 +16,9 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] -configopts = "--enable-cxx" +# '-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"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb index 134d181212255831296c9a1adb305b9e41f99628..9fd3840472384e917e5a856d3bcb14a2228af3f2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index 25f9aacaceb2cbc08c6c99d7f4f2fab8032a3278..222b4603e6d91f68ca6fe1816315cbfaf2d3fa73 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb index 5ca90d16a7bee62a427909a9a79c3c4933481ce4..8d48b943902dd45395d8248a55fd1b0648d6124d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb index 4abe05a74fd0d16c61ffb7ba6dd6672c936745aa..4190871d6ee78291c358e267c371804cccaeded0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2014b'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..a244ff7f0d32c754f9dd457361171520c6b50b32 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +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': 'foss', 'version': '2015.05'} + +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/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb index f58173164e6ea7ee31df0b14fd8d96326a31d73a..6b8e25d1d42559d7b505da0956fd7bd0cf2092e4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index 6a7048dcf1a81e7ed9e3195bdc1bc4e74b11b506..414bbac849b88499423c5944b17aa363068d9fdb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2015b'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..e93393c961bc77670f00ae7b3bd160ffdc1cba6b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +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': 'foss', 'version': '2016.04'} + +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/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index ce563e7def08932c4809c482a06c4c3c99f3ddaa..32fe2f7b787c2f1e5256edbf79b01bf1f9490117 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb index e7ea6f7b851c730a3acb99612b5294fe4fb0f044..3d6737ba0844df35224d64b4791b3038305d375c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index aa806c1087065210003cfcabf47d2bbb61b64de5..04ba474daf3d405ee78469377703cf87323f7f83 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index 304b160de546e23ba7198d1f926052cce3edb377..ca3c0c7b6c868e7f1e51413e8dd50e531f994e65 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index 46c1b375cb08699f4194031bbfb38da5fa5cd760..e8ed91309a368f8bb795180ae758bbb8a41f90a8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index 0289e6c40e65fe26562286578cc747158621bf4c..a896f05992d9ffd1cf83b9424750bfc8fec0a514 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index 857e1b9ffca6ede724bcf7a8a8948c18fcd55f9d..bd224278e8028e427833c158dd02ea97a777a24a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index a805266216045a722e5ca7f7d064c3e65cc97863..942e49510c5e71e41f31807db5125456cc644d64 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index 6746b4b3a40b5725a49d1bb400af40a19392e934..dbdac66931a995d724bf928810361b7b9bdcc49b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb index 899804b18fe298245f2dca804f36be571f10c59b..683e8274c8ce7cfef125f22feed38dbcec3534cc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 4472772492e50783de3c1929f5c2c6f003611f06..2b9dd5a6b802aaa1193273ccb36735ac4431362c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb index a7e7ddf81ea2627f54ee1256d0782307922645ca..d339ed79b83a37832f155aa63944b49b636e753e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} 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 = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6bbaa91c025a1e40ccdcc7a10e992a8d5c05637 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +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': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..2da711ec97374a0180dcb899290ef68fa2bae685 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 2bc8d9c022922f54733c35a70f59eb90fd7c9537..159d8d0173e40d21c1db63119ba323d2da90113d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,6 +15,8 @@ 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 = { diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb new file mode 100644 index 0000000000000000000000000000000000000000..725469edc9f58df3cb6e537527e0426df5253aae --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 7.305 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.305' +versionsuffix = '-with-extensions' + +homepage = 'http://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb index 2f00cc2dbdd56cbaccf6ec72909079dfa281ac5a..013f802b61d35c06296af9ef9d9623eef1e24c9d 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -21,4 +21,9 @@ sources = [SOURCELOWER_ZIP] dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb index 9fb67afb2a35d4301ece629f143a18bb97308aee..05e18b2e8bdc729ddcadc862c4ee4d7b108b81cd 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb @@ -21,4 +21,9 @@ sources = [SOURCELOWER_ZIP] dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0113113d06007fb73f4fb596a38927cc8f1fc3b --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb @@ -0,0 +1,20 @@ +name = 'MATLAB' +version = '2016a' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_92')] + +import os +license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') +license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') +key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7314d95a8c309a0cc696e65ce935f4d5e039e76e --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2016a' + +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_92')] + +moduleclass = 'math' 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 new file mode 100644 index 0000000000000000000000000000000000000000..151037570692b2db27fcad2f653c4f3fe57db5a9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb @@ -0,0 +1,22 @@ +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': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, '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', +] + +builddependencies = [('CMake', '3.6.1')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..65e2ae532f0b9701f88d2e8fb988538358af784b --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.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': '2016b'} +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', '3.6.1')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch new file mode 100644 index 0000000000000000000000000000000000000000..f02824071ea66549311f728a7a6c641cd256f6af --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch @@ -0,0 +1,14 @@ +# Use double for floating point (64 bit) in METIS by default +# OpenFOAM 4 uses doubles be default +diff -ur metis-5.1.0.orig/include/metis.h metis-5.1.0/include/metis.h +--- metis-5.1.0.orig/include/metis.h 2013-03-30 17:24:45.000000000 +0100 ++++ metis-5.1.0/include/metis.h 2016-09-05 11:39:33.004384533 +0200 +@@ -40,7 +40,7 @@ + 32 : single precission floating point (float) + 64 : double precission floating point (double) + --------------------------------------------------------------------------*/ +-#define REALTYPEWIDTH 32 ++#define REALTYPEWIDTH 64 + + + diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c98b95b63b9ec0dde123247e475e4b4cbd2f94a0 --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MIRA' +version = '4.0.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/', 'download')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' + +patches = ['MIRA-%(version)s-quirks.patch'] + +builddependencies = [('flex', '2.5.39')] +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('expat', '2.1.1'), + ('zlib', '1.2.8'), + ('gperftools', '2.5'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin", "share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a8633bccd704c4f4f4d6ed79f77a10c4cf961d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'MPJ-Express' +version = '0.44' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://mpj-express.org/' +description = """MPJ Express is an open source Java message passing library that allows application + developers to write and execute parallel applications for multicore processors and compute clusters/clouds.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] +sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('Java', '1.8.0_92', '', True), +] + +# compile JNI wrapper library as described in docs +# http://mpj-express.org/docs/readme/README +postinstallcmds = ["mkdir %(installdir)s/src/mpjdev/natmpjdev/lib/build", + "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s",] + +modextrapaths = { + 'CLASSPATH': 'lib', +} + +modextravars = { + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory +} + +sanity_check_paths = { + 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..279406579deaaeb3d63dfff20f781c159d473ebe --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb @@ -0,0 +1,29 @@ +## +# 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 +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +name = 'MUMmer' +version = '3.23' + +homepage = 'http://mummer.sourceforge.net/' +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..a3e8ea9b643661e8ea77b79168307c69d944e1b8 --- /dev/null +++ b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'CMakeMake' + +name = 'MUST' +version = '1.2.0' + +homepage = 'http://www.tu-dresden.de/zih/must/' +description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them + to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful + for application developers that want to develop correct MPI applications. This includes errors that + already manifest --segmentation faults or incorrect results -- as well as many errors that are not + visible to the application developer or do not manifest on a certain system or MPI implementation.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/must-release-1.2.0.tar.gz +source_urls = ['http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/'] +sources = ['%(namelower)s-release-%(version)s.tar.gz'] + +dependencies = [('GTI', '1.2.0')] + +builddependencies = [('CMake', '3.0.2')] + +configopts = ' -DCMAKE_BUILD_TYPE=Release -DGTI_INSTALL_PREFIX=${EBROOTGTI}' + +sanity_check_paths = { + 'files': ['bin/mustrun', 'include/mustConfig.h'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..eaaa1eb1ea62c67a08fe3c8248e298848ffb2084 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.4' +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': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +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/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..4817748dbce4a0ad96e5f01aa87b9630764eb507 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.4' +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +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/MariaDB/MariaDB-10.1.17-intel-2016b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe8145c64d07bd909cf4ffe168a9c909032f48ac --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.17' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'MariaDB-10.1.13-remove-Werror.patch', + 'MariaDB-10.1.13-link-rt-for-jemalloc.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('ncurses', '6.0'), + ('jemalloc', '4.2.1'), + ('PCRE', '8.39'), + ('XZ', '5.2.2'), + ('Boost', '1.61.0', '-Python-2.7.12'), + ('libxml2', '2.9.4'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITHOUT_TOKUDB=ON " # not supported with Intel compilers + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..2afcde557085e0d9c14925c3f6cda7bb9399200c --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb @@ -0,0 +1,16 @@ +name = 'Mathematica' +version = '11.0.1' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] + +license_server = 'license.example.com' + +sanity_check_commands = [('mathematica', '--version')] + +moduleclass = 'math' 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 new file mode 100644 index 0000000000000000000000000000000000000000..8152b5bb382a5de704b62c2e15c600cecff34429 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -0,0 +1,59 @@ +# 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 = '12.0.2' + +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': 'foss', 'version': '2016b'} +# 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/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.4', '-Python-2.7.12'), + ('libxml2', '2.9.4', '-Python-2.7.12'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('nettle', '3.2'), + ('libdrm', '2.4.70'), + ('LLVM', '3.8.1'), + ('X11', '20160819'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..90fd4b08106c27fa8e78f82acaf70efea622644f --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -0,0 +1,59 @@ +# 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 = '12.0.2' + +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': '2016b'} +# 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/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.4', '-Python-2.7.12'), + ('libxml2', '2.9.4', '-Python-2.7.12'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('nettle', '3.2'), + ('libdrm', '2.4.70'), + ('LLVM', '3.8.1'), + ('X11', '20160819'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..79a432c81fddef6feecdd91f8e3baaf12adc21a9 --- /dev/null +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -0,0 +1,50 @@ +# 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 = 'Minimac2' +version = '2014.9.15' + +homepage = 'http://genome.sph.umich.edu/wiki/Minimac2' +description = """minimac2 is an improved version of Minimac. It is designed to work on phased + genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. + The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. + The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://csg.sph.umich.edu/cfuchsb/'] +sources = ['%(namelower)s.%(version)s.src.tgz'] + +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 +] + +# firt move to folder libStatGen to run make clean && make +# make clean is mandatory because the sources tarball includes +# files from previous build +prebuildopts = ["cd libStatGen && make clean && "] + +# in libStatGen folder run just "make" +# in minimac folder run "make clean && make opt && make openmp" +buildopts = [" && cd ../minimac2 && make clean && make opt && make openmp"] + +# parallel build fails +parallel = 1 + +files_to_copy = [(["minimac2/bin/minimac2", "minimac2/bin/minimac2-omp"], "bin")] + +sanity_check_paths = { + 'files': ['bin/minimac2', 'bin/minimac2-omp'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb b/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..2bf90d3dc1196c3fd11571ac08be559869158d1c --- /dev/null +++ b/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb @@ -0,0 +1,45 @@ +easyblock = 'PackedBinary' + +name = 'Molcas' +version = '8.0-15.06.18' +versionsuffix = '_CentOS_6.6_x86_64' + +homepage = 'http://www.molcas.org' +description = """Molcas is an ab initio quantum chemistry software package +developed by scientists to be used by scientists. The basic philosophy is is to +be able to treat general electronic structures for molecules consisting of +atoms from most of the periodic table. As such, the primary focus of the +package is on multiconfigurational methods with applications typically +connected to the treatment of highly degenerate states.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download requires registration, see http://www.kvant.kemi.uu.se/molcas/ +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] + +# The Molcas installation procedure creates a binary in a separate directory, +# but that binary depends on being able to find the originally extracted files. +# Because we don't want to rely on root privileges, and we do want to use +# EasyBuild paths, this means we need to extract Molcas to a subdirectory of +# the proposed installation directory. +unpack_options = "--transform='s,^%(namelower)s-%(version)s%(versionsuffix)s,%(namelower)s_files,'" + +buildininstalldir = True +skipsteps = ['install'] + +# For the same reason as the tarball needs an extraction prefix, we need to +# finish up the installation by taking the Molcas driver and moving it to an +# EasyBuild style binary directory. +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin', + 'cp %(installdir)s/%(namelower)s_files/sbin/molcas.driver %(installdir)s/bin/molcas', +] + +modextravars = {'MOLCAS': '%(installdir)s/%(namelower)s_files'} + +sanity_check_paths = { + 'files': ['bin/molcas'], + 'dirs': ['bin'], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..365455df1b7dbd604bfab36be9df48af0c6a1562 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb @@ -0,0 +1,28 @@ +name = 'Mono' +version = '2.10.6' + +homepage = 'http://mono-framework.com' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# Mono required Mono to build, so there are a couple of options: +# 1) provide Mono RPMs in sources, the Mono easyblock will use them to make a tmp Mono install +# 2) assume a Mono version is available system-wide (assert using e.g. "osdependencies = ['mono-core']") +# 3) specify an already available Mono module as build dep, e.g. "builddependencies = [('Mono', '2.10.6')] + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [ + SOURCELOWER_TAR_BZ2, + # Mono requires Mono to build, so provide RPMs so Mono can be bootstrapped + 'libgdiplus-2.4.2-2.el5.kb.x86_64.rpm', + 'mono-core-2.4.2.3-2.el5.kb.x86_64.rpm', +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb index faf00e50147471b0d7281cdd86c9e9b40796c1a2..85b5fe929e1ebbba2837272d6a489b9215cc4275 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb @@ -3,15 +3,20 @@ version = '3.1.2' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." + toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] +builddependencies = [ + ('Autotools', '20150215', '', ('GCC', '4.7.2')), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb index 72d2021690503a362a9d811c0f8130e6e5c0b872..3e3e9603f2e47e57cb5a3ca0cb8843ee25ee327f 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb @@ -4,16 +4,19 @@ version = '3.1.2' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." - toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb index a474900368fbcd9b7bcff9f1b3acf3ac6309433e..1ebf8b83b478363099ce910f3a9c269296827f41 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb @@ -3,15 +3,20 @@ version = '3.2.0' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." + toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('beagle-lib', '20120124'), ('libreadline', '6.2'), ] +builddependencies = [ + ('Autotools', '20150215', '', ('GCC', '4.7.2')), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb index 7ac8ffef36d3fd7da4e32bf0abbdf9b271c4e561..79d0b7f30493bf534c041b6ffc5132e5b4855d8d 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb @@ -4,16 +4,19 @@ version = '3.2.0' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." - toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('beagle-lib', '20120124'), ('libreadline', '6.2'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb index 5836ec7f0f8b87018de0211084f1546aa60dcdce..421c44d0e5cdd9c197b5dfc2b0b0c7b8b672cfa9 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb @@ -5,14 +5,18 @@ homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] dependencies = [ ('beagle-lib', '20141202'), ('libreadline', '6.3'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e098f7c88a1ce36a08907458fbb8b82461618a7d --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'MrBayes' +version = '3.2.6' + +homepage = 'http://mrbayes.csit.fsu.edu' +description = "MrBayes is a program for the Bayesian estimation of phylogeny." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('beagle-lib', '2.1.2'), + ('libreadline', '6.3'), +] + +builddependencies = [ + ('Autotools', '20150215'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..75f50aa79eda43a92fa582b639e35aa0d8a81f1f --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.10' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.mymedialite.net/download/'] +sources = ['%(name)s-%(version)s.src.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe6afff73144f3da1641e96fc665c3bf9e484a04 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.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': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), +] + +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-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..0391b993ae32da1e6241807273c772f9124547c8 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-3.5.2.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': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('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-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..64688cec7b15bf2c85e165f52fddbc2832fd24d4 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.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', '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-1.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..2cd2414697a611bb846f179741519aa4955217b9 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.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': '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'], + }), +] + +# 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-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..1db14993c4f59db29d1c3f43f1776484a6dd0d2f --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-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': 'intel', '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/mypy/mypy-0.4.5-intel-2016b.eb b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7ebbaca141af8c82d6053364f7ff312bbc5b7093 --- /dev/null +++ b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'mypy' +version = '0.4.5' + +homepage = 'http://www.mypy-lang.org/' +description = """Optional static typing for Python""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '3.5.2')] + +exts_list = [ + ('typed-ast', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typed-ast'], + 'modulename': 'typed_ast', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/mypy-lang'], + 'source_tmpl': 'mypy-lang-%(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 + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mypy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..72c77d668585c8b0fe9ee29c38ae4e61004f6d2f --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-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 = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +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/NGS/NGS-1.2.3-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5ebb8f01ff7a93dd7c3a33236849259172272a64 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.3' + +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': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_92', '', 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/NGS/NGS-1.2.5-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b032e04685d6d7fa4f9f651bf9b7e8d8b1c8f5c --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.5' + +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': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_92', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0bd19a1216f1b8e75a8205c068f79f45f2e4280 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.5.8-1' + +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': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.28'), # provides libmagic + ('HDF5', '1.8.17'), + ('NGS', '1.2.3'), +] + +# 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/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..077b870927f75f35b9a59a6e24c9ada988ff0f12 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.7.0' + +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': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.28'), # provides libmagic + ('HDF5', '1.8.17'), + ('NGS', '1.2.5'), +] + +# 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-CrayGNU-2016.03.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb index e38323ffdaec2921572c3dd6a938ad9660e3eedf..307af92999e6a5ffb1b85295ef784a91bf05bf77 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb @@ -14,6 +14,8 @@ 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', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb index 02e4aae6ca6448e09ce92bb015875700f8b569e7..7d6659abd11b9fc4c609c05d7f71df94cecdb71d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb index eab9da36db7595cf134d65292f3571c48391de32..52110246d2c979150effa33c01f679747980af80 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + builddependencies = [('binutils', '2.25')] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 4012f0e69bde30c60bcc4568189782260e4fd448..c1921a50bf7b551ecc59de5d26f821747bdbff8c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb index 6029357e961c47bb3ba2f920abb5b420f48aadce..8036d044c2e6bab2dc4712d6c50fe7ee863d22f1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb index c9773784c0049e4b66ccd35bb64224cbc7fee43c..2e3653e592f93e9244b892ab5e4c421faf95c045 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb @@ -14,6 +14,8 @@ 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', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb index 7c1c8c34c6cf03d24cca678a2ba6004d4122b553..06011329cd05fe88f8255a508b52a22950b33d66 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb index 852b0df6bb6aaa5f84a7f1b4bb27c82b0acf0641..ae4905339165847f3c41738794541599be46a22c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb index 2744e32733401ad9f9739e85f4fd7399669ec88a..d3393acd5476ff8f11fd75a91f4ef6888c12eed6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb @@ -14,6 +14,8 @@ 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', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..98a4144e524698c6d433f23155599de09ef7d413 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb @@ -0,0 +1,36 @@ +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': 'iomkl', 'version': '2016.07'} +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/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..12229c25b54d0d92ca1afa4b5243bf0b1a0daa9a --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 51d2a6f5390b67287c3aac50a949cfbfdfa62761..ce06be716db3d152dd801b16d50764256f444c29 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -14,14 +14,17 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build - '--with-shared --enable-overwrite', + '--with-shared --enable-overwrite --with-termlib', # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --with-termlib ' + + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] -libs = ["form", "menu", "ncurses", "panel"] +libs = ["form", "menu", "ncurses", "panel", "tinfo"] 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"]] + diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5320b4aa4c47317b445f27a209446b7590978927 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.4.1'), + ('netCDF-Fortran', '4.4.4'), + ('UDUNITS', '2.2.20'), + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2016b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8da424609fc2d9eef5a711423effd7dc44d8a710 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2016b.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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..0706679ca3cc77053a00085269cce83aceec46d8 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive'] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..9dd4898f43637d18fd86fd7ba6521172fdf44ca0 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive'] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..a0a822a67343e9057086a019906bb8d620dc849e --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb @@ -0,0 +1,34 @@ +# Automatically converted from netCDF-4.3.3.1-iomkl-2015.03.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +name = 'netCDF' +version = '4.4.0' + +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.46.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), + ('Szip', '2.1'), +] + +# 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-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..eec48bea4ade0fcc07892c575570c4de39657786 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +name = 'netCDF' +version = '4.4.0' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.46.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), + ('Szip', '2.1'), +] + +# 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-foss-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5da2b108a04104d3756795bdca527eb3dd7a9dcf --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.8.17'), + ('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/nettle/nettle-3.2-foss-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d8b0e1009de7d82f3bb5753ead3da9279d97a158 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.2' + +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': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.1'), +] + +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/nettle/nettle-3.2-intel-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..728d2523674a97e20a89edb120aaf765b5290546 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.2' + +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': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.1'), +] + +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-1.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..8dde76eb25208e4ddf70044f8be0369432cd193a --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.11' +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +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-3.5.1.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..488dd6f650b21339163af62a2077156c783b98b8 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.11' +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ced9988f351e47b39ac55f02958aac17d3245e9f --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c5140ef8ceefd40f3addca4905966f73ad112e2 --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..971304f89cbb5206f4072534a9108961d21b164b --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..b862023bd66c4b68fb14486d6d01850ae7c574f9 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.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': '6.1.0-2.27'} + +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-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d6ccf39997b1ba13d214fccdd4942677d5ea625 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.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': '6.2.0-2.27'} + +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'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6d4718450e67621812bac54968825452c16e739 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.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': 'gcccuda', 'version': '2016.10'} + +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-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..61b226e7c458a4903737a582e6dca5f45afdc2b6 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +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': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +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/numexpr/numexpr-2.6.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7f59e992ee1cdfd5451bee33f1db02b56005eb0 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-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': 'intel', '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/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f2a2e65aae5130199e21821266a342e568df4cde --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.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': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.5.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' 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 new file mode 100644 index 0000000000000000000000000000000000000000..d30d6266abf160541580bec17d22186c5b551d58 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'OBITools' +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. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + + +dependencies = [ + ('Python', '2.7.11'), + ('Cython', '0.24.1', versionsuffix), + ('wheel', '0.29.0', versionsuffix), + ('IPython', '5.0.0', versionsuffix), + ('Sphinx', '1.4.8', versionsuffix) +] + +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'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..d50dab2154905f6f81841b49c2d3b4d66d918b3a --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '1.1.1' + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d25cf1b3ab773e9dbbb22a8c62759a0c7b28545c --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.3.2' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..831526692c13f152f7754aaa9db7ed3b3d65c984 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = 'OTF' +version = '1.12.4' + +homepage = 'http://www.tu-dresden.de/zih/otf/' +description = """The Open Trace Format is a highly scalable, memory efficient event + trace data format plus support library. It is the standard trace format + for Vampir, and is open for other tools. [NOW OBSOLETE: use OTF2]""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.4salmon.tar.gz +sources = ['%(name)s-%(version)ssalmon.tar.gz'] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get='] + +# name change in version 1.12.3: "open-trace-format" was "otf" in older versions +# "open-trace-format" => "otf" for versions until 1.12.2 +sanity_check_paths = { + 'files': ['bin/otfconfig', 'include/open-trace-format/otf.h', + # note by Bernd Mohr: on some systems libraries end up in lib/ + ('lib64/libopen-trace-format.a', 'lib/libopen-trace-format.a')], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..335f79d16b292fadb11e42c9d76e2cd02abbe5aa --- /dev/null +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Fotis Georgatos +# License:: MIT/GPL +# +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "MakeCp" + +name = 'Oases' +version = '0.2.08' + +homepage = 'http://www.ebi.ac.uk/~zerbino/oases/' +description = """Oases is a de novo transcriptome assembler designed to produce transcripts from + short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +velvetver = '1.2.10' + +sources = [ + '%(namelower)s_%(version)s.tgz', + 'velvet_%s.tgz' % velvetver, +] + +source_urls = [ + 'http://www.ebi.ac.uk/~zerbino/%(namelower)s', + 'http://www.ebi.ac.uk/~zerbino/velvet', +] + +# listed make targets exclude 'doc' on purpose +buildopts = ['VELVET_DIR=../velvet_%s cleanobj velvet oases' % velvetver] +parallel = 1 + +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] + +sanity_check_paths = { + 'files': ["bin/oases", "LICENSE.txt", "README.txt"], + 'dirs': ["data", "scripts", "src", "doc"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d50479b08d1f01ba90472d53d1ebe3081cdfeb4 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.0.0' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXft', '2.3.2'), + ('PCRE', '8.38'), + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('arpack-ng', '3.3.0'), + ('cURL', '7.47.0'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6.2'), + ('GLPK', '4.58'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.3'), + ('Java', '1.8.0_72', '', True), + ('zlib', '1.2.8'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt', '4.8.7'), + ('HDF5', '1.8.16', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.1', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.23'), +] + +configopts = 'MOC=$EBROOTQT/bin/moc ' +configopts += 'UIC=$EBROOTQT/bin/uic ' +configopts += 'RCC=$EBROOTQT/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..45f3d738e8b42a8fe00fcaba2023b28ff3c3dfad --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.0.3' + +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', '2.6.0'), + ('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', '7.49.1'), + ('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_112', '', True), + ('zlib', '1.2.8'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt', '4.8.7'), + ('HDF5', '1.8.17', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.5'), +] + +configopts = 'MOC=$EBROOTQT/bin/moc ' +configopts += 'UIC=$EBROOTQT/bin/uic ' +configopts += 'RCC=$EBROOTQT/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch new file mode 100644 index 0000000000000000000000000000000000000000..71297e00cffa4fb4b5e57344f8c49ad96fdf38db --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch @@ -0,0 +1,35 @@ +Intel compiler does not understand __builtin_*_overflow +# Oct 25th 2016 by B. Hajgato (Free University Brussels - VUB) +--- octave-4.0.3/libgnu/xalloc-oversized.h.orig 2016-07-01 20:43:46.000000000 +0200 ++++ octave-4.0.3/libgnu/xalloc-oversized.h 2016-10-24 16:05:11.093643937 +0200 +@@ -36,7 +36,7 @@ + sizeof (ptrdiff_t) <= sizeof (size_t), so do not bother to test for + exactly-SIZE_MAX allocations on such hosts; this avoids a test and + branch when S is known to be 1. */ +-#if 5 <= __GNUC__ || __has_builtin (__builtin_mul_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_mul_overflow)) && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) \ + ({ size_t __xalloc_size; __builtin_mul_overflow (n, s, &__xalloc_size); }) + #else +--- 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-4.0.3/libgnu/intprops.h.orig 2016-07-01 20:43:43.000000000 +0200 ++++ octave-4.0.3/libgnu/intprops.h 2016-10-24 16:23:43.652325264 +0200 +@@ -353,7 +353,7 @@ + /* Store A B into *R, where OP specifies the operation. + BUILTIN is the builtin operation, and OVERFLOW the overflow predicate. + See above for restrictions. */ +-#if 5 <= __GNUC__ || __has_builtin (__builtin_add_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + # define _GL_INT_OP_WRAPV(a, b, r, op, builtin, overflow) builtin (a, b, r) + #elif 201112 <= __STDC_VERSION__ && !_GL__GENERIC_BOGUS + # define _GL_INT_OP_WRAPV(a, b, r, op, builtin, overflow) \ 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 new file mode 100644 index 0000000000000000000000000000000000000000..abbe566e013bd20e4cd08f884d58b34f9fd4e360 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.0' +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': '4.9.4-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/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 d8f2e33a1963f19e3e89a827d85ea12f6ad90aaf..9dd493110feae11daf6a9942187ef325ba95fc78 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 @@ -14,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} 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_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] 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 09e78a78ca8747ce20748fd2d3c75134cdd94b9d..3879abb7bd9c821c86536f8d6d9b8618ffac1643 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 @@ -14,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} 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_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] 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 3183ffeabd71899067bc7d3f76b4c3648df0de8b..21a2a7c81548f8ba57987b857d046a7a7f52ac03 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 @@ -14,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} 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_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..80a706fa331223901ad0788e8e9ac0d9152986be --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'gompi', 'version': '2016.07'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..0978b24ceddc792dc43002f640eee0bc7cfccea3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'gompi', 'version': '2016.09'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..55794b44742b487687b77be8810d063d17ba14d8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'gompic', 'version': '2016.10'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +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/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ce69b4afdeff8da5a994b00ebfce08a52a7975c2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +name = 'OpenBabel' +version = '2.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'strict': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'OpenBabel-%(version)s-fix-link-path-tests.patch', + 'OpenBabel-%(version)s-ignore-failed-test.patch', + 'OpenBabel-%(version)s-ignore-rotor-test.patch', +] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), + ('Eigen', '3.2.8'), +] + +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch new file mode 100644 index 0000000000000000000000000000000000000000..8783154988b6bce48b17b5898cceaf49f696303b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch @@ -0,0 +1,12 @@ +# The rotor tests fails, it is removed from the test set. +# Author: Ruben van Dijk (University of Groningen) +--- test/CMakeLists.txt.orig 2016-09-05 15:17:23.000000000 +0200 ++++ test/CMakeLists.txt 2016-09-05 15:17:38.000000000 +0200 +@@ -18,7 +18,6 @@ + implicitH + lssr + isomorphism +- rotor + shuffle + smiles + spectrophore 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 new file mode 100644 index 0000000000000000000000000000000000000000..f835d278f9cff58e89abe02f361b7800e5ac1ccf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -0,0 +1,67 @@ +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': '2016a'} + +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('FFmpeg', '3.0.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('GLib', '2.48.0'), + ('GTK+', '2.24.30'), + ('GStreamer', '1.6.4'), + ('GST-plugins-base', '1.6.4'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..896ae67a98a2e8d242e0323bb40ae44172f07c17 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.1.0' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('FFmpeg', '3.1.3'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('GLib', '2.49.5'), + ('GTK+', '2.24.31'), +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..479f9021cea48fd4b77f603ffbdf1568400402d9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '2.2.0' + +homepage = 'http://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.6.1')] + +env_vars = "CPATH=%(installdir)s/include/OpenEXR:$CPATH " +env_vars += "LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH " +env_vars += "LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH" +preconfigopts = [ + "cd IlmBase && ", + "cd OpenEXR && " + env_vars, +] +prebuildopts = preconfigopts[:] +preinstallopts = preconfigopts[:] + +sanity_check_paths = { + 'files': ['lib/libHalf.so'], + 'dirs': ['bin', 'include/OpenEXR', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..065d8bedfb68191d9ddd9ae619d0bbe9453a1126 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '3.0.1' + +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': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major_minor)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['a6ffe3edabdd23f9eff31be47a092b07'] + +patches = ['OpenFOAM-%(version)s_cleanup.patch'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.4'), + ('CGAL', '4.8.1'), + ('ParaView', '5.1.2', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.6.1'), + ('flex', '2.5.39'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch new file mode 100644 index 0000000000000000000000000000000000000000..9111c18ae37236870a431b74287cdec929ba0e25 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch @@ -0,0 +1,304 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans , Kenneth Hoste +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-3.0.x-version-3.0.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-25 11:51:45.000000000 +0200 +@@ -6,11 +6,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake 2016-10-25 12:00:41.000000000 +0200 +@@ -12,7 +12,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake libso vtkPV3Readers + PV3blockMeshReader/Allwmake +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake 2016-10-25 12:00:41.000000000 +0200 +@@ -12,7 +12,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake libso vtkPV4Readers + PV4blockMeshReader/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/bashrc 2016-11-08 12:21:21.478604080 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/bashrc 2016-11-08 12:21:27.978572000 +0100 +@@ -32,7 +32,7 @@ + #------------------------------------------------------------------------------ + + export WM_PROJECT=OpenFOAM +-export WM_PROJECT_VERSION=3.0.x ++export WM_PROJECT_VERSION=3.0.1 + + ################################################################################ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/cshrc 2016-11-08 12:21:43.478604102 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/cshrc 2016-11-08 12:21:50.258390000 +0100 +@@ -31,7 +31,7 @@ + #------------------------------------------------------------------------------ + + setenv WM_PROJECT OpenFOAM +-setenv WM_PROJECT_VERSION 3.0.x ++setenv WM_PROJECT_VERSION 3.0.1 + + ################################################################################ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/CGAL.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/CGAL.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/CGAL.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/CGAL.sh 2016-10-25 12:04:22.000000000 +0200 +@@ -29,29 +29,5 @@ + # Sourced from OpenFOAM-/etc/bashrc + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=CGAL-4.7 +- +-export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version +-export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version +- +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +-fi +- +-if [ -d "$CGAL_ARCH_PATH" ] +-then +- _foamAddLib $CGAL_ARCH_PATH/lib +-fi +- +-if [ -d "$BOOST_ARCH_PATH" ] +-then +- _foamAddLib $BOOST_ARCH_PATH/lib +-fi +- +-unset boost_version cgal_version +- +-# ----------------------------------------------------------------------------- ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/gperftools.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/gperftools.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/gperftools.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/gperftools.sh 2016-10-25 12:05:33.000000000 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++PERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/metis.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/metis.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/metis.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/metis.sh 2016-10-25 12:06:03.000000000 +0200 +@@ -33,7 +33,7 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/paraview.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/paraview.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/paraview.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/paraview.sh 2016-10-25 12:09:26.000000000 +0200 +@@ -36,29 +36,16 @@ + # clean the PATH + cleaned=`$WM_PROJECT_DIR/bin/foamCleanPath "$PATH" "$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake- $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/paraview-"` && PATH="$cleaned" + +-# determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 + #export ParaView_VERSION=4.0.1 + #export ParaView_VERSION=4.1.0 + #export ParaView_VERSION=4.3.1 +-export ParaView_VERSION=4.4.0 ++#export ParaView_VERSION=4.4.0 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + +- + # Evaluate command-line parameters for ParaView + _foamParaviewEval() + { +@@ -95,16 +82,12 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + if [ ! -d $ParaView_LIB_DIR -a -d $ParaView_DIR/lib/paraview ] +@@ -112,8 +95,6 @@ + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview + fi + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -125,17 +106,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/scotch.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/scotch.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/scotch.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/scotch.sh 2016-10-25 12:12:06.000000000 +0200 +@@ -33,7 +33,7 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/settings.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/settings.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/settings.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/settings.sh 2016-10-25 12:13:20.000000000 +0200 +@@ -87,11 +87,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +@@ -598,6 +598,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-25 12:13:37.000000000 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-25 12:13:37.000000000 +0200 +@@ -119,10 +119,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/scotchDecomp/Make/options 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/scotchDecomp/Make/options 2016-10-25 12:13:37.000000000 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch new file mode 100644 index 0000000000000000000000000000000000000000..6ad12341f4642c621ad241466bab9dfb1f35eac0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch @@ -0,0 +1,291 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.0.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.0/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.0.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-09-02 15:44:36.305512075 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.0.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.0/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-4.0.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-09-02 15:44:36.305512075 +0200 +@@ -16,7 +16,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVReaders + PVblockMeshReader/Allwmake $* +diff -ur OpenFOAM-4.0.orig/etc/bashrc OpenFOAM-4.0/etc/bashrc +--- OpenFOAM-4.0.orig/etc/bashrc 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/bashrc 2016-09-02 15:43:37.773220097 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=${BASH_SOURCE%/*/*/*} || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.0.orig/etc/config.sh/CGAL OpenFOAM-4.0/etc/config.sh/CGAL +--- OpenFOAM-4.0.orig/etc/config.sh/CGAL 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/CGAL 2016-09-02 15:43:37.773220097 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/gperftools OpenFOAM-4.0/etc/config.sh/gperftools +--- OpenFOAM-4.0.orig/etc/config.sh/gperftools 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/gperftools 2016-09-02 15:43:37.773220097 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/metis OpenFOAM-4.0/etc/config.sh/metis +--- OpenFOAM-4.0.orig/etc/config.sh/metis 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/metis 2016-09-02 15:43:37.773220097 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/mpi OpenFOAM-4.0/etc/config.sh/mpi +--- OpenFOAM-4.0.orig/etc/config.sh/mpi 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/mpi 2016-09-02 15:43:37.773220097 +0200 +@@ -243,6 +243,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.0.orig/etc/config.sh/paraview OpenFOAM-4.0/etc/config.sh/paraview +--- OpenFOAM-4.0.orig/etc/config.sh/paraview 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/paraview 2016-09-02 15:43:37.773220097 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.0.orig/etc/config.sh/scotch OpenFOAM-4.0/etc/config.sh/scotch +--- OpenFOAM-4.0.orig/etc/config.sh/scotch 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/scotch 2016-09-02 15:43:37.773220097 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/settings OpenFOAM-4.0/etc/config.sh/settings +--- OpenFOAM-4.0.orig/etc/config.sh/settings 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/settings 2016-09-02 15:43:37.773220097 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ur OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/Make/options 2016-09-02 15:44:36.305512075 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-09-02 15:45:13.376950242 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.0.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.0/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.0.orig/src/parallel/decompose/scotchDecomp/Make/options 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/src/parallel/decompose/scotchDecomp/Make/options 2016-09-02 15:44:36.305512075 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..635072f873d12eb770a87c4a0079ec92b0839bc7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['294b520811aae87241f3a78423f05952'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.4'), + ('CGAL', '4.8.1'), + ('ParaView', '5.1.2', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.6.1'), + ('flex', '2.6.0'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7e6e2a6a220355428cbb3b9baa8ef669a5ad2138 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '1.6.17' + +homepage = 'http://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] +sources = ['Release-%(version)s.tar.gz'] + +dependencies = [ + ('Boost', '1.61.0'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('OpenEXR', '2.2.0'), +] +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.so', 'lib/libOpenImageIO_Util.so'], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..ac26d4212f687dcd9984ba00f094ec6ab2d35089 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +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',] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +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': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' 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 new file mode 100644 index 0000000000000000000000000000000000000000..af22c5f5162eb54544e4b5716251d42f8dc95693 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.3' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +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',] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb new file mode 100644 index 0000000000000000000000000000000000000000..917b1522075b8a9073c4302a0dad0ed95b93f389 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = "1.10.3" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2016.08'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd6bb36c388a4243691b6754ce1cc9e76edf6050 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +checksums = ['fb2fdb6a5b65c80d7dfa4bc9a0caf665'] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.4')] + +# needed for --with-verbs +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 = { + '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': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..c16d7bf245b8a9c1c4e241cab52d2842a1fb89a3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +dependencies = [('hwloc', '1.11.3')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..aeb2a52e4c0da3c43e51233471f368bd31e00e08 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.4')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..3d626a7c8052893e65a9cbef0eb41bc3c5db7b7f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +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',] + +dependencies = [('hwloc', '1.11.4')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible + +# 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-2.0.1-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 new file mode 100644 index 0000000000000000000000000000000000000000..7d74bf0639a5f5668ee1472b3d894b4f888bf1fe --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.1' + +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-5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] + +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-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/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..71a267bdcecee369316f2ef1499276881bfa1143 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.2h' + +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': 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/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..89d8603d595f13122a3301bf9c4e0b4e06ccf404 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.2h' + +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': 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/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..e10bff00048896f519514f0403f819a1795ca5da --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.2h' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': 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/p/PCRE/PCRE-8.39-foss-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.39-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4941ec393583768f6503fdc0a9695df7419fb085 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.39-foss-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.39' + +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': 'foss', '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/PDT/PDT-3.19-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..48f05702911454a17be17a6a5f67f79ca2445604 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb @@ -0,0 +1,32 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'PDT' +version = '3.19' + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] + +moduleclass = 'perf' 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 new file mode 100644 index 0000000000000000000000000000000000000000..4071bc769afd3a3c1f5bd22b32a1a365602e3414 --- /dev/null +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.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='Tarball' + +name = "PGDSpider" +version = "2.1.0.3" +versionsuffix = "-Java-%(javaver)s" + +homepage = 'http://cmpg.unibe.ch/software/PGDSpider/' +description = """An automated data conversion tool for connecting population genetics and genomics programs""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] +sources = ['%(name)s_%(version)s.zip'] + +dependencies = [ + ('Java', '1.7.0_80', '', True), +] + +sanity_check_paths = { + 'files': ['PGDSpider2-cli.jar', 'PGDSpider2.jar'], + 'dirs': [], +} + +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""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..c31c9c139b3e8f315afe79170f716ad63f083e2a --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.10' + +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 = ['9bb6bfb7b1052f9e6a45829ba7a24e47'] + +gccver = '5.4.0' +binutilsver = '2.26' +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/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e4d5e410367b1e6adab6215e386f92b2c9031e6 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('libjpeg-turbo', '1.5.0'), + ('freetype', '2.6.5'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec5fd48964fcc0602f504f9ae010a7f8638e802c --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-intel-2015b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.1.4' + +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': '2015b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '1.16'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c12f858946fb0cc9a03219844fc810175463a645 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-foss-2015b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '1.16'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb25f08bf9e202d2434db9b1f910d3f79b1c90b3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'PLplot' +version = '5.11.1' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://plplot.sourceforge.net' +description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols + and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.6.1'), + ('SWIG', '3.0.10', '-Python-%(pyver)s-PCRE-8.39'), + ('libtool', '2.4.6'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Java', '1.7.0_80', '', True), + ('Python', '2.7.12'), + ('Perl', '5.24.0'), + ('cairo', '1.14.6'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), + ('Pango', '1.40.3'), + ('pixman', '0.34.0'), + ('Tcl', '8.6.5'), + ('Tk', '8.6.5'), +] + +separate_build_dir = True + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], + 'dirs': ['bin', 'include/plplot', 'lib/fortran/modules/plplot', 'lib/pkgconfig', 'share/man/man1'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b01bff9fa68804c7ba08401c73ebec59b6077d43 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb @@ -0,0 +1,56 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, 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 = 'POV-Ray' +version = '3.7.0.0' + +homepage = 'http://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +patches = ['POV-Ray-%(version)s_fix-boost-linking.patch'] + +dependencies = [ + ('Boost', '1.61.0'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('X11', '20160819'), + ('LibTIFF', '4.0.6'), + ('SDL2', '2.0.4'), +] +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch new file mode 100644 index 0000000000000000000000000000000000000000..aac9faf99046adffa7ff78c5403d585b53fc09a4 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch @@ -0,0 +1,30 @@ +also include -lboost_system when linking with -lboost_thread +cfr. https://build.opensuse.org/package/view_file/openSUSE:Leap:42.1:NonFree/povray/povray-3.6.9.7-boost-link.patch?expand=1 +--- povray-3.7.0.0/unix/config/ax_boost_thread.m4.orig 2013-11-06 21:28:15.000000000 +0100 ++++ povray-3.7.0.0/unix/config/ax_boost_thread.m4 2016-09-07 18:26:36.447847499 +0200 +@@ -104,14 +104,14 @@ + for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + if test "x$link_thread" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/boost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + fi +@@ -119,7 +119,7 @@ + else + for ax_lib in $ax_boost_user_thread_lib boost_thread-$ax_boost_user_thread_lib; do + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb index 9d52b0ef8862d6c0d902a9233ff2a19617ba84a3..ed0569f10136967d3595406717d9a1186a9b2438 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -33,8 +33,6 @@ builddependencies = [ ] configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' -configopts += ' -DENABLE_DUMMY_PLUGIN=ON -DCHEMPS2_ROOT=$EBROOTCHEMPS2' -configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' # CMake will pick mpiexec by default and this fails with intel MPI #configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb index 90a88521229e8e33edb85a1604f42913a83a0a05..1fcbf7998b7d8041ce3203c7d9ff413bc3f5f2c5 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb @@ -34,8 +34,6 @@ builddependencies = [ ] configopts = '-DENABLE_MPI=OFF -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_PLUGINS=ON -DENABLE_DUMMY_PLUGIN=ON' -configopts += ' -DENABLE_CHEMPS2=ON -DCHEMPS2_ROOT=$EBROOTCHEMPS2' -configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' # Execute 4 tests in parallel and disable the pubchem tests (they download things and don't work reliable) # Limit the number of concurrent tests to avoid failures diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..70136d70c148a55548e711428c71154dbb478b23 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.1' + +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': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('HarfBuzz', '1.2.7'), + ('GObject-Introspection', '1.48.0'), + ('fontconfig', '2.11.95') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..16a242644026a3c4178633e77a7db3c49977f448 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-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': 'intel', '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/ParaView/ParaView-4.4.0-foss-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffa008562b522cd40f0957e517533ac22aee34ef --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-foss-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '4.4.0' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': False} + +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-source.tar.gz"] + +patches = ['%(name)s-%(version)s_missingheader.patch'] + +dependencies = [ + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('libXt', '1.1.5'), + ('Qt', '4.8.7'), + ('libXext', '1.3.3'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +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 ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' +# 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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb index a0d908d3d55d69410f38d61d4aff340dd04b5786..881a107e714ed81c80fd5315ac80fd7178857abf 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb @@ -27,6 +27,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3'), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.4.3')] @@ -38,8 +39,9 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # 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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb index 2e7bc45270cfcd09fac2f78b3a774424376d2554..5d0a411cd910563f37a70fa62ad000484c3eb956 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb @@ -27,6 +27,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3', pysuff), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.3.2')] @@ -38,8 +39,9 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # 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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb index 0057213bea9baabbefe8efc4c88490e2718989d4..ae3e6cddc3370555ad57175122962bbe12ac3a0d 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb @@ -26,6 +26,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3', pysuff), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.3.2')] @@ -37,8 +38,9 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # 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 $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index 838808a7430e2ff01978cad94497c5f60727f166..0197db69778e703662d1d131a6108e0f6e6951b6 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3'), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.5.2')] @@ -31,6 +32,7 @@ separate_build_dir = True configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..59f802689e29d0a2d004e5cd68c72fe4189d81cf --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.1.2' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.17'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$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 ' +# 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/Perl/Perl-5.22.1-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..873d35ef8aa5207d8157d9f3ff2ca3e83a5b8cf3 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb @@ -0,0 +1,885 @@ +name = 'Perl' +version = '5.22.1' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.60', { + 'source_tmpl': 'Config-General-2.60.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', '2016020301', { + 'source_tmpl': 'Regexp-Common-2016020301.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', '1.02', { + 'source_tmpl': 'DateTime-Locale-1.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.95', { + 'source_tmpl': 'DateTime-TimeZone-1.95.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', '0.4216', { + 'source_tmpl': 'Module-Build-0.4216.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', '1.22', { + 'source_tmpl': 'Params-Validate-1.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.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', '1.25', { + 'source_tmpl': 'DateTime-1.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.01', { + 'source_tmpl': 'Readonly-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('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', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-0.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('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', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-1.44.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.024', { + 'source_tmpl': 'IO-Socket-SSL-2.024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.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', '2.001001', { + 'source_tmpl': 'Moo-2.001001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.15', { + 'source_tmpl': 'Package-DeprecationManager-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9915', { + 'source_tmpl': 'version-0.9915.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-1.31.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': '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', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('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', '1.33', { + 'source_tmpl': 'XML-XPath-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.36', { + 'source_tmpl': 'Capture-Tiny-0.36.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', '2.000002', { + 'source_tmpl': 'strictures-2.000002.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', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.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', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.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', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.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', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.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', '1.43', { + 'source_tmpl': 'Scalar-List-Utils-1.43.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', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('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', '2.1605', { + 'source_tmpl': 'Moose-2.1605.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', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.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', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9156', { + 'source_tmpl': 'CPANPLUS-0.9156.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', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.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', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PhyloBayes-MPI/PhyloBayes-MPI-20161021-intel-2016b.eb b/easybuild/easyconfigs/p/PhyloBayes-MPI/PhyloBayes-MPI-20161021-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7fb0e0c330bc6e02efde602693801d2f9317e3d0 --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloBayes-MPI/PhyloBayes-MPI-20161021-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'PhyloBayes-MPI' +version = '20161021' +commit = 'e4ea1ca' + +homepage = 'https://github.com/bayesiancook/pbmpi' +description = "A Bayesian software for phylogenetic reconstruction using mixture models" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/bayesiancook/pbmpi/archive/'] +sources = ['%s.tar.gz' % commit] + +start_dir = 'sources' + +# get rid of included binaries to ensur they're recompiled +prebuildopts = "rm -f data/* &&" + +buildopts = 'CC="$MPICXX" CPPFLAGS="$CXXFLAGS -c" LDFLAGS="$CXXFLAGS"' + +files_to_copy = [(['data/*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bpcomp', 'bin/cvrep', 'bin/pb_mpi', 'bin/readpb_mpi', 'bin/tracecomp'], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..16cea8d33bff1c5a9fdadaab7d0087a532e2a26b --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.2.0' +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +freetype_ver = '2.6.3' +versionsuffix += '-freetype-%s' % freetype_ver + +dependencies = [ + ('Python', '2.7.11'), + ('libjpeg-turbo', '1.4.2','-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', freetype_ver), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..4667d2c7a639ec629da41ab9d2497a92a1bcd648 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.4.2' +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.26'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.7'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..8573700cd509ca6a846a697f2d7ad118417c05b8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2-freetype-2.6.5.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.4.2' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +freetype_ver = '2.6.5' +versionsuffix = '-Python-%%(pyver)s-freetype-%s' % freetype_ver +dependencies = [ + ('Python', '3.5.2'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', freetype_ver), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..a95d247bb56abfca54e08afd1bcf77e3112727fe --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.4.2' +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.26'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.7'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..30ff748dc8c05e6ff5995466fd16db636884eb56 --- /dev/null +++ b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'CMakeMake' + +name = 'PnMPI' +version = '1.2.0' + +homepage = 'https://scalability.llnl.gov/pnmpi/' +description = """MPI Tool Virtualization and Interoperability library.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/pnmpi-for-gti-1.2.0.tar.gz +source_urls = ['http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/'] +sources = ['%(namelower)s-for-gti-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.0.2')] + +configopts = ' -DCMAKE_BUILD_TYPE=Release -DBFD_FOUND=False -DPNMPI_HAVE_BFD=False' + +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/pnmpi-patch", "include/pnmpi.h", "lib/libpnmpi.a"], + 'dirs': [], +} + +moduleclass = 'perf' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a1b0d0ba132ea1bc0e9021233c255bcf924163a6 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.mysql.com/' +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.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +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 +] + +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/PyQt/PyQt-4.11.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..b495a5ba45473287484c34d62a3f261d26f19105 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-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 = '4.11.4' +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'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +dependencies = [ + ('Python', '2.7.12'), + ('SIP', '4.18.1', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f366cc75cac90c041f739540d7823d194fe0c80 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.7' +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': 'foss', 'version': '2016a'} + +sources = ['%(name)s_gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] + +dependencies = [ + ('Python', '2.7.11'), + ('SIP', '4.18.1', versionsuffix), + ('Qt5', '5.7.0'), +] + +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-3.0.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb similarity index 98% rename from easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb rename to easybuild/easyconfigs/p/PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb index 929534794765b79fb7ade3f3fab468b6af23d5e6..2a4a81773022537ee7003fc93a56730137988afd 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb @@ -1,6 +1,6 @@ easyblock = "PythonPackage" -name = 'pyTables' +name = 'PyTables' version = '3.0.0' homepage = 'http://www.pytables.org/moin' diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb similarity index 83% rename from easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb index c7500dde1e317bc1a9fe958c1b870f7fbb7f5ccd..554e1e9785d35df5a356b8fbec4e6c569bec103f 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb @@ -1,7 +1,8 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = 'pyTables' +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 @@ -20,13 +21,8 @@ sources = ['v.%(version)s.tar.gz'] patches = ['pyTables-%(version)s-fix-libs.patch'] -python = 'Python' -pythonver = '2.7.10' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) - dependencies = [ - (python, pythonver), + ('Python', '2.7.10'), ('numpy', '1.10.4', versionsuffix), ('numexpr', '2.4.6', versionsuffix), ('HDF5', '1.8.13'), @@ -34,7 +30,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], - 'dirs': ['lib/python%s/site-packages' % pythonshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } options = {'modulename': 'tables'} diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb3c5f680e1ef5c9584e60975a71b64669d33b0f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.3.0' +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/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..28dfb8ca71d9fd8796df11b018646ccf57d4e1e0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.3.0' +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', '3.5.2'), + ('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/pyTables/pyTables-3.2.2-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/pyTables-3.2.2-fix-libs.patch similarity index 100% rename from easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-fix-libs.patch rename to easybuild/easyconfigs/p/PyTables/pyTables-3.2.2-fix-libs.patch diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..72a7f70320c5cac148b8772b105b538ec76c053e --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('libyaml', '0.1.6'), +] + +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-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..266c49b4251ba6c4a87959956b4637096f09c914 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..f2cb9702842be3b42bf6772691ad30360ad36bc6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.4.0' +zmqversion = '4.1.5' +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': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('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/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..85869f21eaaa3fbe57b298e3559e82d58cb66d20 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a1e3fec180dbc3354e023396037b9b73948b1b2 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pyro4' +version = '4.47' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/Pyro4' +description = """Pyro means PYthon Remote Objects. It is a library that enables you to build applications in which + objects can talk to eachother over the network, with minimal programming effort.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +options = {'modulename': 'Pyro4'} + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a77cac29a1f406af02f679735052fd7319bfde2 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,53 @@ +# 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 = 'Bundle' + +name = 'Pysam' +version = '0.9.1.4' +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': 'foss', 'version': '2016b'} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.12'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('Cython', '0.25.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'bio' 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 c19c8970457265734e48c582d48254519bd9c0ab..fd80fddc40f51885bb2f75b08a277357e590e513 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] 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 094f5e83b06bb0f33397874d5ed0a5ad815fc64d..6e9aa1f7c47660e47380b7076dd42ab4a25fdf0a 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] 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 2110e24871ad60fa20c219404a6e3267868524df..f325e4238c084f9bbcb9daf528289518580225d8 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 76db705ebd43c5cb0af06dbf7336ff68a6cd2fad..1ba18083e712967aac8c27f4a69400d4d60b3289 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 a5549be2988dac0021bea2cddf1a5771f2aaac77..e615c893547f7581d6d0ea217240b46b5298f574 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] @@ -66,7 +66,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 1156ffc2af46661292bc90d9725cd9ae06ccf773..7d445cd6ba97ba7c57b211b7ef67ea2b5e60912e 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 56b2274143f301040e8858e71cff60578c8af7b2..55f10df08f8cecd11049a2dd1f1ce546742abd20 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 2661d5c96a779fadeb6fd65af456eaf45aa0aac1..017e1ecaae37816c1851bad94eee84625e6283db 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 94c61afabcb5d86a3a178d1a125564ec96ec188f..276aa8a0f36f3b5512cd64fcca87869f10ab6291 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] @@ -66,7 +66,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 9a52c8f87de7c0c5ed82bfc3e31d566c36c92d13..d69b594b089801a7bd59378bb50da618d38a2fda 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 @@ -26,7 +26,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ] 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 99f60636cbab3f4770cbb3276ed290c18fa5fbc5..ab13993dcf3d948857fd3edf0ea84defe533da8a 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 @@ -26,7 +26,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ] 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 895d73b12812161ba0da64981aaf3b314695d6f9..78953148b07d0b7ce8e840e283640a66e9de5f00 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 @@ -19,7 +19,7 @@ dependencies = [ ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] 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 7e7c21223925235b457e71a5c67cdd6a89ddfc25..60154d0a99cd9ed62ea83b43f89739d4d64abb68 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.10.0'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # 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 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 3e1f1e63c683f6a13b9cb92f84a1e54f21e5a111..cd19e3b9026c69ba6f6a5e731913f47eb938b85e 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 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 5bee9397c43c552432d27651f4438d58879e4ad1..917a362739fd79c5678fd76ce1d3fa0bdc8cce76 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 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 98314b77b5a9cd8beda96745dc4397cf3d28c8c0..974e57d87ccf7d6bed4132d8b6676c90eb846b24 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 @@ -21,8 +21,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), - ('Tk', '8.6.4'), + #('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 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 71a4890e4705fb727f25a97513e903ab16116101..fa2f05cdb99f521fc1e8fead8461872d3c14e45b 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 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 bb7d002230ca8db62b3e890b4bf5888fabbde878..914f184b700fba5cf55706ed96bb8eaaf4f052d2 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 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 8ab42a8b9f0ba35dafb531679c1ca11fd8de7849..711240b058aa2e3cc29a758de72c54d476383e1a 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 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 new file mode 100644 index 0000000000000000000000000000000000000000..c445811709b702b1a22d832603067c1257a6921a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -0,0 +1,139 @@ +# Automatically converted from Python-2.7.11-foss-2016.09.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +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.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack + ('Tk', '8.6.4'), # this requires a full X11 stack + ('GMP', '6.1.0'), + ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + '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', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('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/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('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/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + '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', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000000000000000000000000000000000..ed40bed006921b98e3aecb20bd26f6a7c381c164 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,137 @@ +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.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack + ('Tk', '8.6.4'), # this requires a full X11 stack + ('GMP', '6.1.0'), + ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + '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', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('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/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('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/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + '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', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb index fb337a3d58372791eccf7cdbc6f6830e0f8f7e45..abfcbbf934634e4ace5d77d23dfee715d6e5bd50 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('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, 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 8bb576da7d5d1bbe9d9f6dbf33f13fa78fd6eda6..ba6ada1467237aadd0d98828506e50c9df09c353 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('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, 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 e77dca81729da570931c589ec1ff4425ee8029c5..f39ab1c05674d776d582c462884cdb54b6e8a21c 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('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, 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 7bff359058f43cd65ee21d95630b9dfac5e985f9..c93dab2804d6cb744950e58678dedee6163e9b56 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 b20ffd67fb5a575df71ea292f4311d513348378b..53cdae92ab860f1520daa0dcf5adbc905e1de3d1 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 e087117a23517b8593e77efc650e6d5ab0885944..4cd83e24d0f4f969bca9df91ed373f3813d24834 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 65a7050c90012aff70fd707e967d49c12fdf221f..2608210a179afdb4d3b1bef1a2d58ac585adfda2 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 caf683b0c800a39ac4c46a2ed461893496c59dfa..4ffdd56f7800b9dc5fe39837cf155cc71df044b6 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 a68ef18929ba692311f25818eb3b4ee67222dba0..35bbb975535d761680a4fbeb9aaa492d999190e1 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 577653d1f500a18b89a14dd896c88ae5e42f1961..d2f51e3f225383ac22796fe0120c29b86eb84b48 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 @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 33dce6f6ca70c4d163a55494fbf6981104a7e7e4..c0ac0d38b167ed567979672a19c5672e53a35e19 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 @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 0a01b973a0d04f9d8e749f177468080d522ea9de..513384d5b56bc8f6840351d13429524f1ddfafb8 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 @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 bccfcbf0c220159d4884b052b8db0902e5103c5c..95ff34f3f9c16d4f92b6b515b58e529aa605393c 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.19.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 a51d51c98601d8e4aa4dde8345eadbd9f37cc522..055543dc247f6c4468e7ca6846a42848857008e2 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 @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.19.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 16590efbbd1082d005bcc7366f17bb28f2fb5612..0409f54975348bd1829001623869731240213a96 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 c8491023d824a0fcc9f8df18b857d9996fc9d82a..2a90fee410794f5472b4c01a1c78db08ab1183f0 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 @@ -66,7 +66,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 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 a7caba4faefa586132a5cf7a48abbfb0b1d111ea..d975d85c2d94c09a0ea9204032b84d4f49994824 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 @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 dfe5979c7c5be91e27fee21819b96e4ba29932b4..dca27371ed7ee6aca17c27df12cd50399816331a 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 @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 54121e1a6fb6163021e9322e44f936839b68a2fa..a7d56bba1649ef4c244ff86e1dd958201539f86f 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 @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 012b08cef627b9559ee0ebc3552e7fc9b8ebc540..6b2fccea289c94605fb2568bf089930788156a6b 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 @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 21613bcfb7b1f115bba75831af9747b1f6e81e94..2c98486b9278bd013e550fc5097f3dbf4141222b 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 @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 995830889256293017fc2801333def200068bdfc..23449c08344b745ab07671f6003efe17ff6cbdca 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 @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 new file mode 100644 index 0000000000000000000000000000000000000000..c83dff187b29fb8cd1c5af5288e12872b6480914 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +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." + +toolchain = {'name': 'GCC', 'version': '4.8.4'} +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', '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 +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' 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 3b6c965221828caceed13fe34a8a081458be763a..a2e4addace20b764cda53531311ae544a52539bd 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] 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 75386ccc4ae440fdd476204f4c3bac846ed86504..5ca1dda84ebf4921cc24b0bb1e3ecf64c7d3da76 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 a04b4992d3845721e9864bf8d50cb8c820db2ecb..e9063410dfeec2b3c5d8c206c2e47b6735d06fe9 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] 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 4d8258d2814dbe834747b4bb981629fdccda846c..b636f6b2ef65feaf08d11a7020afa201bb16d9dc 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 81bfd4da015806761f8fba3af718cd1078262272..82282d02d9c59b7288f88b1ce95ff78f21429ccf 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 e8eb88c738b8515c0acdd92406529736f5761d62..c78274679f6a502ace6591f31b60967423a4895c 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 @@ -17,7 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] 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 7739e8b255f28286877c996601b1401b193d72bf..987f0852f63aeadfb8be7fa65388f8638c396336 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 70860e49fae83bae772200301bb1c9ac2afe26f4..37abf12093b638069fb0196b2261d71c61207510 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 41e6d0cc85a0022e8ea63d0e19670a50af085be3..7bdd55756a3bea354c50eb16cead6dc8314a6128 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f327891d4e89bb2eac7544a33b0072fb19e7b9ae..c672a429fd7839f1081602d1c9aa0105c75aefbd 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] 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 188046b96972413bb51af944e7b138d6b414e563..24081c5cf8cd659ccc7f85ef90ab0dc64dc1c0e8 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('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 ] @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 98e26ec9ef9e2640d46dee45dde04b8860cec7a9..fc5033662d8a96ec9887f5b14c299ec6a7fbbad3 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 @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 4bc546cccb224feaeff993eaddb52f7136206643..1fe945390aa2e1dd00c7315e29103136c803670a 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 @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 66630e998024756b4c660470994c00aa39f69aa8..ba9c2f40b215f23b21e3e540c5788b9642ac80e3 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 @@ -66,7 +66,7 @@ exts_list = [ 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 d93f95e46a11c395573086dbc367b1b4ae459b4e..910cb21e5cf0a7003b352fee17cfbc94d01fa9c5 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 @@ -66,7 +66,7 @@ exts_list = [ 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f8a3851092f9de828685b73cb6076653b39571ab..8f08cf73e46a4cf26573fed8045f552886a425ed 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 @@ -63,7 +63,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 6b562baa0c5a440a364a9665f8b470d3b6713b5a..825c8e6b10acc1a20d3bd1204053a834129f1d6e 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('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 @@ -66,7 +66,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.23.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 c11711336fab9a27acfda522da1aee2e14e1959b..129c326cbbd9b44389316069cf5ac5a2ad3940ad 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's @@ -66,7 +66,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.23.4', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f0600eefc0fcfb7da096b2802d560121632bc252..395e40515b102c6def7ff6326907eafd508bc59d 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 @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.23.4', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 new file mode 100644 index 0000000000000000000000000000000000000000..f49b2ff08519ec0a3549129deefd04a9d163b443 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -0,0 +1,123 @@ +name = 'Python' +version = '3.5.2' + +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': '2016.04'} +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'), + ('XZ', '5.2.2'), + ('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', '1.0.2h'), +] + +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/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('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/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('virtualenv', '15.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' 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 a637288eb8fb5a0c82479c5108490743944921a0..f40c4aab551a331325e3f14f233d4673bd4a6ae4 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('XZ', '5.2.2'), ('libffi', '3.2.1'), @@ -56,6 +56,9 @@ exts_list = [ }), ('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', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -76,6 +79,9 @@ exts_list = [ ('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', '4.0.10', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 46d7ae7573d22e6961a27876aa589bd689daddca..805061ab30b31af53ad2e6564cfa0550060d6e4f 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('XZ', '5.2.2'), ('libffi', '3.2.1'), @@ -56,6 +56,9 @@ exts_list = [ }), ('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', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -76,6 +79,9 @@ exts_list = [ ('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', '4.0.10', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..d10a536e673b74a9535fbc843d218550b106bb5c --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'foss', '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/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..66017ec4037993a827fccf7651103f13883c852a --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..8829139b1b7111dfeac12dffc7a7771cf95be1c6 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +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/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..823a55912c7d24fb730fb79fd80bc83781620c51 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..2d89267d1dbe0318bfef69088cbd0992eb5db57b --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +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/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..15fd3118b30e2c7465369de5bb754cb88f5c5bbe --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f558dad06a9f860c348c1aadc150701e5c952d18 --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +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': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/fc/fc/dcae2146aed6becbea77158eddb4e437718170efeade0f7fdf0aebe46b94/'] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), +] + +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/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb new file mode 100644 index 0000000000000000000000000000000000000000..c89d3af9f2898475e971cf1fecf04ac52cf3ccc7 --- /dev/null +++ b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb @@ -0,0 +1,34 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'Conda' + +name = "perl-app-cpanminus" +version = "1.7039" +variant = "Linux-x86_64" + +homepage = 'https://github.com/miyagawa/cpanminus' +description = """ cpanm - get, unpack build and install modules from CPAN """ + +toolchain = {'name': 'dummy', 'version': ''} + +requirements = "%(name)s=%(version)s" +channels = ['bioconda'] + +builddependencies = [('Anaconda2', '4.0.0')] + +sanity_check_paths = { + 'files': ['bin/cpanm', 'bin/perl'], + 'dirs': ['lib', 'lib/perl5'] +} + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000000000000000000000000000000000..9ac838302496c32bdafd1c7cebf9e759da69bfc7 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb @@ -0,0 +1,18 @@ +name = 'picard' +version = '2.1.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.8.0_112')] + +modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae4b777250d2b4ec846f97ea6d0f5ab2dbbd8bbb --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-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': 'intel', '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-foss-2016b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7e76d6460337d4492f7d841833270ab2688ab213 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016b.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': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.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-1.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..2723e2f049a57e278b1cfcf6ca4d02081474a297 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +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': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('pkg-config', '0.29.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb new file mode 100644 index 0000000000000000000000000000000000000000..74076e42f0edad261eac72a05846074f5bb8e9bc --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.09' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.7' +gccsuff = '-GCC-5.4.0-2.26' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.4', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb new file mode 100644 index 0000000000000000000000000000000000000000..b83ba47007df4fd52384234739cc11340ab71ed2 --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.09' +pgisuffix = '-GCC-5.4.0-2.26' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.7' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.4', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a9b5ed1e232531cedceba2574a6dad033864f94e --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb @@ -0,0 +1,39 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.11' +bioperl_ver = '1.7.0' +versionsuffix = '-BioPerl-%s' % bioperl_ver + +homepage = 'http://www.vicbioinformatics.com/software.prokka.shtml' +description = """Prokka is a software tool for the rapid annotation of prokaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] + +dependencies = [('BioPerl', bioperl_ver, '-Perl-5.24.0')] + +modextrapaths = { + 'PATH': '', +} + +bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + '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" + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..6c89475fe0bc1ce19f8c2efbb6b497691e15c2dd --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +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': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/eb/81/a7ad3c223f323d05381208c262889bd09577852bd5044a13965a9a13f5ed/'] +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), + ('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/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 new file mode 100644 index 0000000000000000000000000000000000000000..3deb45334a2f85f8443163e0b58018d33a49bbfb --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.0.2' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('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-3.0.2-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 new file mode 100644 index 0000000000000000000000000000000000000000..64b04ec53c33de2b066e44ce7ae2b22d0076a4d9 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.0.2' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..14ba425f1fd6f47f11fa6dc44dc3a4a3eb6675eb --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.0.2' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +preconfigopts = "./autogen.sh &&" + +sanity_check_paths = { + 'files': ['bin/protoc','lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b8241e929e157bfd88ab3d3f946c6b0e43a7f93 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '4.1.1' +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('spglib-python', '1.9.4.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ff5f953560c7769c76eba605e3a24b6922a2ed74 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pymatgen' +version = '4.3.2' +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('spglib-python', '1.9.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6422b82abed50d558bb7ed8e8a996508a11ed199 --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb @@ -0,0 +1,29 @@ +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': 'foss', 'version': '2016a'} + +source_urls = ['http://delta.affinix.com/download/qca/2.0/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.5.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c145ad7bf0649471287adeb0aa73d4b0cc32bbe0 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Recently changed the Unix version numbering see http://www.qhull.org/src/Changes.txt +# and https://github.com/Homebrew/homebrew-science/issues/3353 +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e282e73b715b93b524bdfe75f05ea361b50eded4 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull-%(version)s-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.6.2')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a342ad59982a235fba7af0f12ecc7ed6291ed00 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016b'} + +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', '0.29.1'), +] + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1ccc867425d0adf0186dbb51f651016dbf6a82f3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +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'] + +builddependencies = [ + ('fixesproto', '5.0'), + ('glproto', '1.4.17'), + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('pkg-config', '0.29.1'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a387649d5b91fea6359ece25f0f2e6bccb220305 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +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'] + +builddependencies = [ + ('fixesproto', '5.0'), + ('glproto', '1.4.17'), + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('pkg-config', '0.29.1'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..589ca4e25a966d3c7afd8b9863f76100bee87d3d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': '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 = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch new file mode 100644 index 0000000000000000000000000000000000000000..fd58176f43c91bfad349d0f5425cc2afd7ef31dc --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch @@ -0,0 +1,62 @@ +# This is an ugly workaround for a icpc bug: https://software.intel.com/en-us/comment/1882560 +# If the struct/class is local, icpc gives a faulty error. We move the class to be non-local. +# Remove this patch as soon as icpc is fixed. +# Ward Poelmans +diff -ur qt-everywhere-opensource-src-5.7.0.orig/qtdeclarative/src/quick/items/qquickitemanimation.cpp qt-everywhere-opensource-src-5.7.0/qtdeclarative/src/quick/items/qquickitemanimation.cpp +--- qt-everywhere-opensource-src-5.7.0.orig/qtdeclarative/src/quick/items/qquickitemanimation.cpp 2016-06-11 14:05:08.000000000 +0200 ++++ qt-everywhere-opensource-src-5.7.0/qtdeclarative/src/quick/items/qquickitemanimation.cpp 2016-08-29 12:42:35.880738297 +0200 +@@ -200,6 +200,27 @@ + } + } + ++struct QQuickParentAnimationData : public QAbstractAnimationAction ++{ ++ QQuickParentAnimationData() : reverse(false) {} ++ ~QQuickParentAnimationData() { qDeleteAll(pc); } ++ ++ QQuickStateActions actions; ++ //### reverse should probably apply on a per-action basis ++ bool reverse; ++ QList pc; ++ void doAction() Q_DECL_OVERRIDE ++ { ++ for (int ii = 0; ii < actions.count(); ++ii) { ++ const QQuickStateAction &action = actions.at(ii); ++ if (reverse) ++ action.event->reverse(); ++ else ++ action.event->execute(); ++ } ++ } ++}; ++ + QAbstractAnimationJob* QQuickParentAnimation::transition(QQuickStateActions &actions, + QQmlProperties &modified, + TransitionDirection direction, +@@ -207,26 +228,6 @@ + { + Q_D(QQuickParentAnimation); + +- struct QQuickParentAnimationData : public QAbstractAnimationAction +- { +- QQuickParentAnimationData() : reverse(false) {} +- ~QQuickParentAnimationData() { qDeleteAll(pc); } +- +- QQuickStateActions actions; +- //### reverse should probably apply on a per-action basis +- bool reverse; +- QList pc; +- void doAction() Q_DECL_OVERRIDE +- { +- for (int ii = 0; ii < actions.count(); ++ii) { +- const QQuickStateAction &action = actions.at(ii); +- if (reverse) +- action.event->reverse(); +- else +- action.event->execute(); +- } +- } +- }; + + QQuickParentAnimationData *data = new QQuickParentAnimationData; + QQuickParentAnimationData *viaData = new QQuickParentAnimationData; diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd4f2fd67f9551719be835e71ed975fe69039c01 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb @@ -0,0 +1,55 @@ +name = 'QuantumESPRESSO' +version = '6.0' + +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': '2016b'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'qe-gipaw-6.0.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', + '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://qe-forge.org/gf/download/frsrelease/224/1044/', # qe-6.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.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 = [ + 'e42aeeffadf7951542d8561a6b4a3390', # qe-6.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + 'b11a8b75109eb58fd97a1c6f7cf20e31', # qe-gipaw-6.0.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.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 gipaw want yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c96735e498d1a0573a4aab2c0c4b76eed79150d --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..004c178582be56e6841d2bfbf8f2992141629f95 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -0,0 +1,449 @@ +name = 'R' +version = '3.2.3' + +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" +# 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 = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.23'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('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 +] + +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 January 21st 2016 +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', '0.6-5', ext_options), + ('abind', '1.4-3', 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', '3.9', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2.1', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-22', ext_options), + ('mime', '0.4', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', 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', '1.7-3', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-1', 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), + ('checkmate', '1.6.3', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-4', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.0.2', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.3-0', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '1.0-1', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.8', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.6-1', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-36', ext_options), + ('SparseM', '1.7', ext_options), + ('tripack', '1.3-7', ext_options), + ('irace', '1.07', ext_options), + ('rJava', '0.9-7', ext_options), + ('lattice', '0.20-33', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-3', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.12.2', ext_options), + ('RcppArmadillo', '0.6.400.2.2', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-1', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.5-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-7', ext_options), + ('nnet', '7.3-11', ext_options), + ('nlme', '3.1-122', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.5.1', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.19', ext_options), + ('mgcv', '1.8-10', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-5', ext_options), + ('sp', '1.2-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.38-3', ext_options), + ('mice', '2.25', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-12', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.3', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.18-1', ext_options), + ('codetools', '0.2-14', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-66', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.3-2', ext_options), + ('gamlss.dist', '4.3-5', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-5', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-3', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.7', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-4', ext_options), + ('sfsmisc', '1.0-28', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-0', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-0', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.2.0', ext_options), + ('R.matlab', '3.3.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.3.0', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '2.0.0', ext_options), + ('gridExtra', '2.0.0', ext_options), + ('Hmisc', 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ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-11', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-5', ext_options), + ('statmod', '1.4.23', ext_options), + ('miscTools', '0.6-16', 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', '1.0.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.50.1', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-10', ext_options), + ('pbkrtest', '0.4-4', ext_options), + ('car', '2.1-1', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.4', ext_options), + ('modeltools', '0.2-21', 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', '2.9', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.9.1', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.1.3', ext_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('VennDiagram', '1.6.16', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-2', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.8-37', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.44-1', ext_options), + ('rgdal', '1.1-3', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.8.8', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), + ('SuperLearner', '2.0-15', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-64', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.6', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.7', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-7', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.10', 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', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.1-2', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.5.8', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-20', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.8-6', ext_options), + ('mi', '1.0', ext_options), + ('htmlwidgets', '0.6', ext_options), + ('visNetwork', '0.2.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-6', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), + ('geepack', '1.2-0.1', ext_options), + ('lubridate', '1.5.6', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), +] + +moduleclass = 'lang' 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 5a44f1a48c8caa0b1f2312717e6870c18f6ae5af..1a886a00c96e84d063a6b2cbd8d934ee6c2540c4 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 @@ -15,8 +15,6 @@ 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=yes --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 diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb new file mode 100644 index 0000000000000000000000000000000000000000..db82fd5e9ad2e6e614f2b1ad240bb4863290df12 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.9' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-HYBRID-AVX2"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..a768f518aca6f9b3cf209673f80748068d3319c8 --- /dev/null +++ b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'RDMC' +version = '2.9.5' + +homepage = 'http://code.icecube.wisc.edu/' +description = "The AMANDA-era RDMC physics library" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://code.icecube.wisc.edu/tools/distfiles/%(namelower)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [('texinfo', '5.2')] + +modextrapaths = {'LD_LIBRARY_PATH': 'lib/rdmc'} + +sanity_check_paths = { + 'files': ["bin/cpfeil", "include/rdmc/rdmc.h", "include/rdmc/rdmc.inc", + "lib/rdmc/librdmc.a", "lib/rdmc/librdmc.so"], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb new file mode 100644 index 0000000000000000000000000000000000000000..add5ffc72c4a6f87e160e00c8485947eca5a8c20 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'RELION' +version = '1.4' +versionsuffix = '-single' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True} + +source_urls = ['http://www2.mrc-lmb.cam.ac.uk/groups/scheres/1sep15/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['RELION-%(version)s_fltk-config.patch'] + +dependencies = [ + ('X11', '20160819'), + ('FFTW', '3.3.5'), + ('FLTK', '1.3.3'), +] + +# RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries +configopts = '--enable-mpi --enable-float ' +configopts += 'LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig -lXinerama -lpthread -lX11" ' +configopts += '&& ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' +# users expect the maingui binary to be called relion +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..74acae10a1b8c00249fced0cdd7fc4af5808fcd0 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'RELION' +version = '1.4' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True} + +source_urls = ['http://www2.mrc-lmb.cam.ac.uk/groups/scheres/1sep15/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['RELION-%(version)s_fltk-config.patch'] + +dependencies = [ + ('X11', '20160819'), + ('FFTW', '3.3.5'), + ('FLTK', '1.3.3'), +] + +# RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries +configopts = '--enable-mpi ' +configopts += 'LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig -lXinerama -lpthread -lX11" ' +configopts += '&& ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' +# users expect the maingui binary to be called relion +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch b/easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch new file mode 100644 index 0000000000000000000000000000000000000000..22a822811f4d53e4fc8879ef4cb3575d99b39fef --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch @@ -0,0 +1,11 @@ +--- configure.orig 2014-08-11 17:18:31.686813247 +0200 ++++ configure 2014-08-11 17:18:39.390957858 +0200 +@@ -15846,7 +15846,7 @@ + #Check for FLTK + # as g++ seems needed and not gcc for compilation, + #just check for presence of fltk-config program +-fltkfile=`pwd`/bin/fltk-config ++fltkfile=`which fltk-config` + as_ac_File=`$as_echo "ac_cv_file_$fltkfile" | $as_tr_sh` + { $as_echo "$as_me:$LINENO: checking for $fltkfile" >&5 + $as_echo_n "checking for $fltkfile... " >&6; } diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a14ff8652cc1fba560af0c7e8e5530229150922 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.0.1' +commit_id = 'a6225608e270' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True} + +source_urls = ['https://bitbucket.org/tcblab/relion2-beta/get/'] +sources = ['%s.tar.gz' % commit_id] + +builddependencies = [ + ('CMake', '3.6.2'), +] + +dependencies = [ + ('X11', '20160819'), + ('FFTW', '3.3.5'), + ('FLTK', '1.3.3'), +] + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..5420a22996be198b95a6a16494b0f93c3f8d0fea --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.2.30' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['RSEM-%(version)s_makefiles.patch'] + +skipsteps = ['configure'] +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +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'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..506890dce28fea86bceb7244e506c77f0584270b --- /dev/null +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.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 = 'Tarball' + +name = 'Reads2snp' +version = '2.0' + +homepage = 'http://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools' +description = """reads2snp is a SNP and genotype caller: it predicts the genotype of distinct individuals + at distinct positions of a set of sequences based on read mapping / read counts. Its typical input is a bam file. + Its typical output is a vcf file. It is written in C++, based on the bio++ libraries, multi-threaded with openMP, + available under Linux and MacOS""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://kimura.univ-montp2.fr/PopPhyl/resources/tools/'] +sources = ['%(namelower)s_%(version)s.zip'] + +sanity_check_paths = { + 'files': ['reads2snp_%(version)s.64.bin'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': "", # add the installation dir to PATH +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..dc1928028ee8ed6ed233f735c488dd6d2789cddd --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb @@ -0,0 +1,20 @@ +name = 'Rosetta' +version = '3.7' + +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')] + +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f97bed944ca236687dbcd46c7bc4592b2cdaf61d --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb @@ -0,0 +1,63 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.3.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +ext_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.10', ext_options), + ('childprocess', '0.5.9', ext_options), + ('json', '1.8.3', ext_options), + ('cabin', '0.8.1', ext_options), + ('backports', '3.6.8', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.0.0', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.9.2', ext_options), + ('faraday_middleware', '0.10.0', ext_options), + ('highline', '1.7.8', ext_options), + ('net-http-pipeline', '1.0.1', ext_options), + ('net-http-persistent', '2.9.4', ext_options), + ('multi_json', '1.11.3', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.14.0', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.8.1', ext_options), + ('typhoeus', '0.8.0', ext_options), + ('websocket', '1.2.3', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.2.5', ext_options), + ('rspec-support', '3.4.1', ext_options), + ('rspec-mocks', '3.4.1', ext_options), + ('rspec-expectations', '3.4.0', ext_options), + ('rspec-core', '3.4.4', ext_options), + ('rspec', '3.4.0', ext_options), + ('rack', '1.6.4', ext_options), + ('rack-protection', '1.5.3', ext_options), + ('tilt', '2.0.2', ext_options), + ('sinatra', '1.4.7', ext_options), + ('rack-test', '0.6.3', ext_options), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000000000000000000000000000000000..de615e762046ffe34e4e7caaa5df4b9a0703f9a0 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.12.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +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')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a06ae545970e984f20cca5d3cae9c30b2009edf5 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.12.1' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +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')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..1435fab7e53a660665edf278a39301f94d2e1d5d --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests/%(version)s' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/requests-%(version)s-py%(pyshortver)s.egg'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..28824ad2fc145f27799888b2467814d8c31f3333 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +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/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..19001f1fa644e9882e9015740266e5131d9bfb85 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1402be8df0cd92d82878530e9cc0b77077edb9db --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2016b.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.19' + +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 = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf342e2224a2bffe8f71631180fb715e368d0b2c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.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:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +# include proper HTSlib dependency rather than using HTSlib version included with SAMtools +htsver = '1.3.2' +versionsuffix = '-HTSlib-%s' % htsver + +dependencies = [ + ('HTSlib', htsver), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-htslib=$EBROOTHSTLIB' + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..9fb7233435ac8a04fcfe74efffabd6129bbc8f47 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb @@ -0,0 +1,14 @@ +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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..20bc255b1a92698416894bcafc8849611455feb1 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb @@ -0,0 +1,14 @@ +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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..f7cac2e6e23485df57afe728788309fb6936a3bd --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.0' +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-2.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..87b42067554d7d732a2e0c38069c7771cff3d335 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.0' +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/SDL2/SDL2-2.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d089f04eb6ce8fe5e556c92a0fe0929a3eeee15 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, 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 = 'SDL2' +version = '2.0.4' + +homepage = 'http://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..756efd9115ca042ae4c7f5d226444872eb54a26e --- /dev/null +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'SHORE' +version = '0.9.3' + +homepage = "http://1001genomes.org/software/shore.html" +description = """SHORE, for Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/shore/files/'] +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'), +] + +sanity_check_paths = { + 'files': ['bin/shore', 'bin/shore-mpi', 'lib/libshore.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ac8c1861dc319fa5edca39d8d3b4a8316e22ae2 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.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 = '4.18' +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': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.11')] + +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-4.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..dbc48b8044d8de9956052828588f23750d75e32a --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.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 = '4.18.1' +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': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.11')] + +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-4.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..57997a86bf365f99400571c661a8530c48d1fe1e --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-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 = '4.18.1' +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/SPAdes/SPAdes-3.9.0-foss-2016a.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..af3845c60d3667cb3aab66edc57688e12c25a5ae --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.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 = '3.9.0' + +homepage = 'http://bioinf.spbau.ru/en/spades' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://spades.bioinf.spbau.ru/release%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +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/SPAdes/SPAdes-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a92f27ffacdc39c0c7ff8d172e787286fe62de0c --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-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 = '3.9.0' + +homepage = 'http://bioinf.spbau.ru/en/spades' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://spades.bioinf.spbau.ru/release%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +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/SQLite/SQLite-3.13.0-foss-2016.04.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee0989cdf47ed8c704440cd282ede5d793f06632 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.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:: 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': 'foss', 'version': '2016.04'} + +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] + +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-3.8.8.1-GCC-4.8.4.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..27cd84d7ec041f654f7d5fd0ed068d683fce9431 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb @@ -0,0 +1,38 @@ +## +# 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 = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..4eb223b17f20c195ec640ef4c8ce7c0a35924c15 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.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:: 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 = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'iomkl', 'version': '2016.07'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +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-3.9.2-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 new file mode 100644 index 0000000000000000000000000000000000000000..e099c4dd67528427a7fb11f85d0f374ee564aeec --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.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:: 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 = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +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/STAMP/STAMP-1.2-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb index 117f2476d8f9cbcf26f751e7a91a5a6b9ebef90b..f3009cafcc3dcecf3dd7c29b72f93d4f6b4fc386 100644 --- a/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb @@ -3,19 +3,19 @@ easyblock = 'CmdCp' name = 'STAMP' version = '1.2' -homepage = 'ihttp://www.benoslab.pitt.edu/stamp/ - https://github.com/aertslab/stamp' +homepage = 'http://www.benoslab.pitt.edu/stamp/' description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https://github.com/aertslab/stamp/archive/'] +source_urls = ['https://github.com/seqcode/stamp/archive/'] sources = ['v%(version)s.tar.gz'] dependencies = [('GSL', '2.1')] start_dir = 'src' -cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp -lm -lgsl -lgslcblas")] +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] files_to_copy = [(['stamp'], 'bin')] diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4eb03dff0151993df6eef1c7149c03c7f61f97d9 --- /dev/null +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'STAMP' +version = '1.3' + +homepage = 'http://www.benoslab.pitt.edu/stamp/' +description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/seqcode/stamp/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GSL', '2.2.1')] + +start_dir = 'src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] + +files_to_copy = [(['stamp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stamp'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..51a70d8dc1935078c4a31bfa57aa3dfaa7e25291 --- /dev/null +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'STAMP' +version = '1.3' + +homepage = 'http://www.benoslab.pitt.edu/stamp/' +description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/seqcode/stamp/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GSL', '2.2.1')] + +start_dir = 'src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] + +files_to_copy = [(['stamp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stamp'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index 79841574824ac44256ab1cc50406beface9a6f6a..44cf8f84ff4a407078896fbbcee923a88ec5bc8f 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -22,13 +22,15 @@ cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 - cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " # 1 billion array elements (1000 runs): requires ~22.4 GiB of memory cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " cmds_map = [('stream.c', cmds_str)] -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B'], 'bin')] +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B'], 'bin')] sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B'], + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B'], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..94341c99a0d9ce7fb9683c5895f858a9e77df41e --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'http://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.virginia.edu/stream/FTP/Code/'] +sources = ['%(namelower)s.c'] +checksums = ['dd2941e3a28ff90a79b571273c10aacf'] + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..db3419830f5ab9f2b4680be554026e3a51a07b68 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.6.2' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', '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/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc435288bd692c5b2db6b91320165710f772507b --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-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': 'intel', '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/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1d01b931eaa4c86804cd6c242a4ba8a42d67814 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.10' +versionsuffix = '-Python-%(pyver)s-PCRE-8.39' + +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', '8.39'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..5345e933136727d79222013a00b8fd3df7ad431a --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2016.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.1' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..8fcb8f66106bf4b89be675ad3f334aad7b9d071e --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2016.09'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..daad463a99bd6af978c67572f704f8ca5432bc8b --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.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': 'gompic', 'version': '2016.08'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.4-2.25'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10-OpenBLAS-0.2.19-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10-OpenBLAS-0.2.19-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..a4526fee655b60bfafbf71252c742615274ae7af --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10-OpenBLAS-0.2.19-LAPACK-3.6.1.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompic', 'version': '2016.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..df0333c95eb5cb399e5a0ca56b8df61e9e322fd1 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = 'Score-P' +version = '1.2.1' + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +sources = ['scorep-%(version)s.tar.gz'] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +# compiler toolchain depencies +dependencies = [ + ('Cube', '4.2'), + ('OPARI2', '1.1.1'), + ('OTF2', '1.2.1'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), +] + +sanity_check_paths = { + 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', + ('lib64/libscorep_adapter_mpi_event.a', 'lib/libscorep_adapter_mpi_event.a')], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb new file mode 100644 index 0000000000000000000000000000000000000000..7fd49e7b9f61b2a54b7e387737d697d441f94c9f --- /dev/null +++ b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb @@ -0,0 +1,35 @@ +# 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 = 'SelEstim' +version = '1.1.4' +versionsuffix = '-Linux-64bits' + +homepage = 'http://www1.montpellier.inra.fr/CBGP/software/selestim/index.html' +description = """SelEstim is aimed at distinguishing neutral from selected polymorphisms and estimate + the intensity of selection at the latter. The SelEstim model accounts explicitly for positive selection, + and it is assumed that all marker loci in the dataset are responding to selection, to some extent""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/selestim/files/'] +sources = ['%(name)s_%(version)s.zip'] + +postinstallcmds = [ + "rm -fr %(installdir)s/__MACOSX/ ", + "mv %(installdir)s/SelEstim_%(version)s/* %(installdir)s ", + "rm %(installdir)s/bin/SelEstim_1.1.4_OSX64bits ", + "rm %(installdir)s/bin/SelEstim_1.1.4_Linux32bits ", + "cd %(installdir)s/bin/ && ln -s SelEstim_%(version)s_Linux64bits SelEstim ", +] + +sanity_check_paths = { + 'files': ['bin/SelEstim_%(version)s_Linux64bits'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..d9e07f44c5058cab4e04b0655c165e609e652d7d --- /dev/null +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.3.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'SimPEG' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://simpeg.xyz' +description = """Simulation and Parameter Estimation in Geophysics: a python package for simulation and gradient +based parameter estimation in the context of geophysical applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +options = {'modulename': 'SimPEG'} + +sanity_check_paths = { + 'files': ['bin/TreeUtils.pyx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6727139e3ee550bbeea6d96cc6efadad19ee9a31 --- /dev/null +++ b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'SimVascular' +version = '2.16.0406' + +homepage = 'http://simvascular.github.io/' +description = """SimVascular is an open source software suite for cardiovascular simulation, providing a complete + pipeline from medical image data to 3D model construction, meshing, and blood flow simulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# download via https://simtk.org/project/xml/downloads.xml?group_id=188 +sources = ['SV-linux-x64-2016-04-06.tar.gz'] + +dependencies = [ + ('X11', '20160819'), + ('Tcl', '8.6.5'), + ('Tk', '8.6.5'), +] + +unpack_options = '--strip-components=1' +keepsymlinks = True + +# mimic what setup-symlinks.sh, but stick to dedicated install dir +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "ln -s %(installdir)s/Bin/simvascular %(installdir)s/bin/simvascular", + "ln -s %(installdir)s/Bin/svpost %(installdir)s/bin/svpost", + "ln -s %(installdir)s/Bin/svpre %(installdir)s/bin/svpre", + "ln -s %(installdir)s/Bin/svsolver %(installdir)s/bin/svsolver", +] + +sanity_check_paths = { + 'files': ['bin/simvascular', 'bin/svpost', 'bin/svpre', 'bin/svsolver'], + 'dirs': ['Bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb b/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb975b50f83bd95c22494970366d87b28a382b11 --- /dev/null +++ b/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Adam Huffman +# The Francis Crick Institute +easyblock = 'MakeCp' + +name = 'SolexaQA++' +version = '3.1.5' + +homepage = 'http://solexaqa.sourceforge.net' +description = """SolexaQA calculates sequence quality statistics and creates visual representations + of data quality for second-generation sequencing data. Originally developed for the Illumina system + (historically known as “Solexa”), SolexaQA now also supports Ion Torrent and 454 data.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(name)s_v%(version)s.zip'] +source_urls = ['https://sourceforge.net/projects/solexaqa/files/src/'] + +dependencies = [ + ('Boost', '1.61.0'), + ('zlib', '1.2.8'), +] + +start_dir = 'source' + +files_to_copy = ['%(name)s'] + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb b/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..8f5ba9118167a1e6211c9ce41f7fff6e895e49a3 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '2.0.2' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.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/', +] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..249a32fcb839a9090b3a23c7bfa34ce6116eb6fb --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,74 @@ +easyblock = 'Bundle' + +name = 'Sphinx' +version = '1.4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('Pygments', '2.1.3', '-Python-%(pyver)s'), + ('requests', '2.10.0', versionsuffix), +] + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Docutils', '0.12', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + }), + ('Babel', '2.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + ('alabaster', '0.7.8', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + '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', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + }), +] + +# Sphinx unit tests *after* installing extensions +postinstallcmds = [' && '.join([ + "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", +])] + +# 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/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..90efc667c60d47c5693a020997438c95fda1fce5 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,74 @@ +easyblock = 'Bundle' + +name = 'Sphinx' +version = '1.4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), + ('Pygments', '2.1.3', '-Python-%(pyver)s'), + ('requests', '2.10.0', versionsuffix), +] + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Docutils', '0.12', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + }), + ('Babel', '2.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + ('alabaster', '0.7.8', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + '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', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + }), +] + +# Sphinx unit tests *after* installing extensions +postinstallcmds = [' && '.join([ + "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", +])] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch new file mode 100644 index 0000000000000000000000000000000000000000..44705787c3adfd7b54238a0754e917ac4ecfeba8 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch @@ -0,0 +1,20 @@ +pdflatex and latex tests fail on systems that have older versions installed +Author: Ruben van Dijk (University of Groningen) +--- Sphinx-1.4.8/Makefile 2016-10-05 11:05:34.000000000 +0200 ++++ Sphinx-1.4.8/Makefile 2016-10-05 11:11:05.000000000 +0200 +@@ -67,8 +67,14 @@ + reindent: + @$(PYTHON) utils/reindent.py -r -n . + ++# Failing tests, py35 was already excluded. ++DONT_TEST = -I py35 \ ++ -I latex \ ++ -I typing_test_data \ ++ -I ext_math ++ + test: +- @cd tests; $(PYTHON) run.py -I py35 -d -m '^[tT]est' $(TEST) ++ @cd tests; $(PYTHON) run.py $(DONT_TEST) -d #-m '^[tT]est' $(TEST) + + test-async: + @cd tests; $(PYTHON) run.py -d -m '^[tT]est' $(TEST) 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 new file mode 100644 index 0000000000000000000000000000000000000000..424d2b7aebc3f281cdd096d43352700945858870 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.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 = '1.3.0' + +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': '2016b'} + +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/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a80824b3c6b63349c3b6b77cbac948076aeccb8 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '4.5.1' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5235dd9545c45fde42a5e6abc637f9bebbe444cd --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '4.5.3' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf50049e0fcbcc785822c6405df7d1e05c0f41cd --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} +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 new file mode 100644 index 0000000000000000000000000000000000000000..512dbbe733f7f257e0767a8adad7c4554a0c594f --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'optarch': True, '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-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..30b672563639c4268aa8902a7e56a38dad4d054a --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'optarch': True, '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.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f0de6e8da6dd329dfe04b5f8674fe79774bad4b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'scikit-image' +version = '0.12.3' +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': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +freetype_ver = '2.6.3' + +dependencies = [ + ('Python', '2.7.11'), + ('Qhull', '2015.2'), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-%s' % freetype_ver), + ('networkx', '1.11', versionsuffix), + ('Pillow', '3.2.0', versionsuffix + '-freetype-%s' % freetype_ver), +] + +options = {'modulename': 'skimage'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..7741dcce3863e723a378d402fde40668b6f53865 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'scikit-image' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('Qhull', '2015.2'), + ('matplotlib', '1.5.3', versionsuffix), + ('Pillow', '3.4.2', versionsuffix), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], + 'modulename': 'skimage', + }), +] + +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/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0eef4a235d1c1f7b836f365e693826e59789e9c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'scikit-image' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('Qhull', '2015.2'), + ('matplotlib', '1.5.3', versionsuffix), + ('Pillow', '3.4.2', versionsuffix), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], + 'modulename': 'skimage', + }), +] + +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/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..948220fce8bc69fb6971e22af82221b1a39a9f6b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +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', '1.5.1', 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-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..cedad0e0ae1c6f481943a7f8e5a2e8b0efdce914 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18' +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', '1.5.1', 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-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..a4cbd2262285302172a6a8a3f6c3575652d2feef --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18' +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', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.2-foss-2016b.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ff933e459c85fd251a3be83f3b04b3c11e0dcec8 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.2-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'seqtk' +version = '1.2' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/lh3/seqtk/archive/'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +files_to_copy = ["seqtk"] + +sanity_check_paths = { + 'files': files_to_copy, + 'dirs': [], +} + +modextrapaths = { + 'PATH': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..2cbf7eff9e3f01a516431bf758f95239f86fa3dd --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'spglib-python' +version = '1.9.4.2' +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': '2016b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..7dd378ce55e82006fdc9c010569dbdc7448e7f49 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.9.5' +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': '2016b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000000000000000000000000000000000..2f2888a832174aa297859e7d9d12b4723cdbf17d --- /dev/null +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = 'TAU' +version = '2.22.2' + +homepage = 'http://tau.uoregon.edu' +description = """The TAU Performance System is a portable profiling and tracing toolkit + for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), + ('Score-P', '1.2.1'), + # obsolete backends, use Score-P instead + #('Scalasca', '1.4.3'), + #('VampirTrace', '5.14.4'), +] + +# scalasca and vampirtrace backends are deprecated +extra_backends = ['scorep'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb index c8585dbd410e6b80b9b2c862b0b81ef0e814cb96..2fb940fc61b1f6d6e8e1a78b3614f2da8b5b99d9 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb @@ -5,7 +5,8 @@ version = '8.3.5' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb index 32fe48b93c8bbcef7aa707d2b576e81eef7c7236..79ab065024950e8a4a66e013be79a3878fb3362f 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb @@ -5,7 +5,8 @@ version = '8.5.12' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2014b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb index 7c9d9e8066b479113fbbe5948731748244197504..dbd46e992ac55ea4d2ecea8643018a60494e4c1f 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '8.5.12' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb index 19f101522b812c49b4f2f67cb43a5ffbcd30502c..7c87bd01fd8764c810dfdeb94cae361a3c31de0c 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '8.5.12' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb index 35f9095bc846555dee3184b20b400a68d295db16..a2241ff65fac51fec9fe67dd7a299d94f5a54d17 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb @@ -5,7 +5,8 @@ version = '8.5.12' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb index ca1465be0bc3c164cd1c680f16eb95b917ff5e0f..e7614a78343a51fd516eb6ead8384510106a2116 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb @@ -5,7 +5,8 @@ version = '8.5.12' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2014b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb index 3e317dec24164c653e7f0cdfb20499ad2c69d68e..f339e9e06f7d11ef4ed5fec4ffc0ff54970ba895 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '8.5.14' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb index 5e237ee8341119d81ad812eda6527ee5fdc7b11d..8e3c92be6bd36f55fec6564f0128e6fbb1b30cd8 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '8.5.14' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb index 78a978f384dd83e07d5dcc93488c2ec3c5b00adb..820b74eea5b641087b3dcd6c9bbd95a1df45b703 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '8.5.15' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb index f46eebeee8bfc33c05645f839661fe6983b6f011..a62da8c0a04b75b0a4340e02f752310a67b11f17 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb @@ -5,7 +5,8 @@ version = '8.5.16' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb index 39ddf4b3a85fc00e0adcb483c06c9e683b53d5db..a560004738cee9868419d3f1bfc0952d91a24ea9 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '8.6.1' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb index 1392ae5cc854f2b4f099876679a30b7f013d0c93..60d6ac83f47acc87eec4acf68ca8130285a12afc 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '8.6.1' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb index 8c3980c54e6b0d6005f8788f29286f2141b2b975..db36da55f6f0f3f49892f1fc967faca762b460fd 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb @@ -5,7 +5,8 @@ version = '8.6.2' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb index 7a5ef170a5a798a23c029ce19d172068fc5fc81c..60cb2b1b9452ae133e8dbde3aa04f3bb0593bd89 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb @@ -5,7 +5,8 @@ version = '8.6.2' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2014b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b4e305153eb0df9625a87daadebff1ee9fa7dba --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +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': 'GCC', 'version': '4.8.4'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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-8.6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb index b3a8beb76754f0bf381e230749f474a100175801..c4d2010766a17e70dd769f9aa9d32de469d108a5 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb index bd202e0e1bf8a43b6fd3ea50ee862a587774a3e8..bf1d49997483ef2dbcd16a5221ecbffe5db28402 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2015.05'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb index 45613c8d4eb729ba28db24345ab191ed9e2756bd..16e045859c55a0278fd63ba63ed3dc45b2da7aa9 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb index ec3f168cb039674794ae6b632c44130c20da3cc4..46e9e125bbd7bd9341767a7b764afb993f34f558 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2015b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb index 5aa437f5739dde3207c632e189c4aec46dd5ecfd..ee5b42935fd4624c6d96ed7dba65ee9a3f200bad 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'gompi', 'version': '1.5.16'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb index f169881758c6ee6a8ae1a5815021adb52ff3b601..1238368e89d75e3d2da9208b39963f10eb2e6e33 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb index a8f55caa258ca7fd3630ae0625e92b5eb5adacc1..dee69d837b4aca415211fcc486f4258dfc076a55 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb index 41060701af9d916894364e98bb050cbfe6e2e6ed..c19a00ca5785d6bebc8967f77091b5bb1b7bafd1 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb index 945189208ba1f45c96341de57ff972f87fab9a99..ab41f83d76185eb28bf0ed2b1c11077d192c9b40 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb @@ -5,7 +5,8 @@ version = '8.6.3' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb index 0a0ed38e5614b1324721d7bc9a180034e946ccb6..37cac05971ca295976e12935cd875ef7022dd5d7 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2016.03.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2016.03.eb index b72c2fc21c4280234abc647d43e1b89a59aff66b..8211069c61bf6ba656017c07b84aa789834df14e 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2016.03.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.3-2.25.eb index e7800ee7009ceb2171117823bcb56487751b030c..1a1dd7dcd565d0d19778ec679b4e2bb1a995a9f7 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.3-2.25.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb index b0ebdff41b7f2cc34534af8f4ad8fddc5c388d2c..5046ee4992206aa4334d6c677770e1d57b226838 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb index d1a6b6efb26e8bf4f455a9d38d6b9aec575cc312..40a19f82a3832a6161e4b961a887da0e6ec47e41 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb index ba9826c847cd16c54dd51efc766448bb74559faa..d067d918e3efc1eff6e3934f6463f2d55bf59b88 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2015b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb index 3884765bf6d968110796c595db9c1ad5248da8f5..c3671ebebfb5e17b1dbaf59ecc4a83632eae5bf4 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gimkl-2.11.5.eb index 154b3e9e279b6a36dc237dc8751a817407f02119..6e056f40fdf71d9744a1b236e55005768d559598 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gimkl-2.11.5.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb index fe02a2bc48eb5b655c5b8cf32493aa2a126492d7..be5009eda98a28937e968fe77c1d20801d7b11a2 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb index e2124cc24dd1bd2fd38f2e70acc86afe3d7ba90f..ff3e6c81671153c24ddca40bd23b34fd9285328f 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb index ab1bbc53d31b00003a7e6f78f26dedd3ebaa3230..df8dfb36e7d62b3b3a5db7148606d90662a434b7 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb index b2673863fdd00046885a98f13efe2283adfbd6ad..c5eceb0d1fa560d83ca3765b599d12b1eb345dce 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb index ae2268790f4ac75746b456e016e11d0644a77515..869c8a60db7671d7abb2356a84e4e52c632c60d5 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb index c2af97cc03dea1065723352512a4554529866e6e..11676da053b17e372e51cb007babdcca4576709e 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb index 20cd9eb96c2310f2e3f22495f770121a1d5580a0..1851e0e5929c74194fad9ec562dbd56c40a2a34a 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb @@ -5,7 +5,8 @@ version = '8.6.4' 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..e35e81b24e2866ffbca3da7bc899db4b003a6ed0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +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': 'iomkl', 'version': '2016.07'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..88e6740d0583f502de3226f271f634d1d06c7460 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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-8.6.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-4.9.3-2.25.eb index bb197b61b9ecae3371c3444b7b8628e236eec6c8..3f4c4832f3b5f24ec33651b94acaf45c96b66873 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-4.9.3-2.25.eb @@ -5,7 +5,8 @@ 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb index cee27f6687d1da49504020a744ff09a4658712d8..0c3128d6576615a262bcd6722bd87428f0e8b1e2 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb @@ -5,7 +5,8 @@ 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..3de05133417ec4a0a302450cd19d38a350b05a60 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb @@ -0,0 +1,26 @@ +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': 'foss', 'version': '2016.04'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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-8.6.5-foss-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016a.eb index 1dc1677c3418a0480283c7aec01a81d127cab2a8..f15e62a824cc9a2101144dea4dd964881b16ba20 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016a.eb @@ -5,7 +5,8 @@ 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016b.eb index d91801e33e8d0543b442155334224fc92415b33c..ee88524e1eef501c160fa443c532d8f565b8f978 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016b.eb @@ -5,7 +5,8 @@ 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-intel-2016b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-intel-2016b.eb index 4691e322fe43aea00106bdea39bd33adde5b9737..b9bb3175fadac1ea38ec2217e8974bccbc04961b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-intel-2016b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-intel-2016b.eb @@ -5,7 +5,8 @@ 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb index 35b772ac6fe5ec4ae051d7e25104d7b502aa3f19..d71a52e8c4a3ff2f98da6afbdd8854d06c2f61e3 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb @@ -5,7 +5,8 @@ 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.""" +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..84985c3bcb7126c067eb925e2a8c4c16b484984d --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] + +# The tests take very long to finish (they are installed too) +#runtest = 'nosetests theano' + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7e9b83bcb9cbf429db94e448c27c4a792c997f4 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] + +# The tests take very long to finish (they are installed too) +#runtest = 'nosetests theano' + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..fdea58014edf8eae5f55812b0e4cdc646fc2f675 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] + +# The tests take very long to finish (they are installed too) +#runtest = 'nosetests theano' + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..e49d8019731bd8028e16866de4924d7757789384 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +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': 'GCC', 'version': '4.8.4'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +# To be clear: this will still require X11 to be present (see issue #2261) +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 878cfecf539d646a638f0b8f90d28410385cf192..df6346fdf8622c8e9503fe82059b23062d45cc8d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index ac0d5ff0bc58a0e2f7efdbe52cfabba110d843de..2394a098151702f035de2c4b3cef43d01965d149 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb index 0cf00324c8d649766fad5967e9794558f037a2d4..89e750afa3e21edababfa75c4bb9ac9e81539971 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb index aaa247a658e841075ccf657058923034df57ed0d..fd29c3376270cf467961a9cb3a50c29444bd9c06 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index 0a860475e3a929120bf43a487276972f0ab382df..be1ac13f469b7c8ef5e74344a76c50fb192b5c84 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index 890bfc8cfec32b0627a4d40f78c98c23034c6716..d5880a0b406cb57a1dcc82bfbc835080a5de45ce 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb index b383831c92fded663690e6735d912d4c17da5103..3fa9a767388661cceaf27a2b19c776333098b462 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb index 6550c8a4272aae568c43a719c928274e112fa044..dccd1a9e2f04d107c498399d646ef55f23264413 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb index 4762abfa095708143bfa749c830771ed12595793..68317abed0de62772800f589d8823d1e3b86853d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb index 75434aa7b825fdf55e7795a1f557b98863603d48..02c810f4e3a3606b5b7ed58257e4cf71ad42c47f 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb @@ -19,6 +19,7 @@ dependencies = [ ('Tcl', version), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb index ce3ef51b8f2ad54cce5b4f29dd29761bdd7a7587..f156bb1a1bfb7ed620ac2e3a11a6d239794add9d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb @@ -19,6 +19,7 @@ dependencies = [ ('Tcl', version), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb index 684f3bddb6d76797e80e073834fabe10633b28f7..8a30be2061d2e140b4943693c2aee12ea8045365 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb index f077e32cc2b099813bcb2191c1e443ad992302c8..50d6e6345589496884fdd0a5a6d72e3816a94b60 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb index 9e3efc89f0dc13cb698825dab87212b0fededf94..2c44f99045c10c3a0cf8d54665c520c2cbc7f941 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb index 89ecb3248a7f4e9dce91b5bc0eec5c35e1a2c1f5..9f80c4ee639c1f17625fb5363a59da3442ec752c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb index 449ce63a291d4ec9eb0aac0d59a6661d24209b0f..57e512249bd8913a8904446510420987fccef12b 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8') ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb index 5066a5847cdc83a938ae04c5379d39b8250933ca..be28b60358aa4d4e1f75e2fd5c63d4b61e3de8ce 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb index 9419fc66d665b810ae7d63238e24e46a8b55a2f8..a88315f8074faefe518850239b00ee95ad64e104 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb index 60f899a5847ab6810b112495340ca502882db963..26804627ae58cc057fe3ad07e48224f9c73f2637 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb index 53f70e54d2f08380c80b58970e26344af25494bd..3e9e1cab39dbb361e6bbaac8c283d367cb0f7baf 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb index 85504f868894a39e812f0577bb5c1392aad3fc40..ff4e4051ee19522145e222265b2ec32315f4dbca 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb index b7e6c77202038c6e9a8ee624284d0696e6f63d44..389d3ddf9828c1c61b2d5e0d615eec3c29ba811b 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb index ed76be27b657422d65a66165fe8979706a5fc259..873aa2d811e2437f6646a1670388bccee1c7b35a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb @@ -19,6 +19,7 @@ dependencies = [ ('Tcl', version), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index 9eede4921066c4045fe7939309e3bef44725eb76..3174f88f273bd3fdea80f8c8aca978720f18d1b9 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb10fedcae8d7678308bbb252d548989c845db70 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +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': 'iomkl', 'version': '2016.07'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +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-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6e7e7c9ce91c1edcba0a739e9b8ba37986aded25 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +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-8.6.5-foss-2016.04.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..5587e8e8dc2b6f3a9e831c8ede461977f23cd820 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb @@ -0,0 +1,26 @@ +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': 'foss', 'version': '2016.04'} + +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 = [ + ('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/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6070a5118ccdd21f5250e204c1fc89dc50aee8c --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb @@ -0,0 +1,33 @@ +# 0.4.2 modified by: +# Adam Huffman +# The Francis Crick Institute +# TODO: deal with the hardcoding of /usr/bin/perl + +easyblock = "PackedBinary" + +name = 'Trim_Galore' +version = '0.4.2' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" + +dependencies = [ + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('cutadapt', '1.9.1', '-Python-2.7.12'), +] + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb index cb200231af407837329f36c8f40d7cb47e0df0d8..30c58df38b902b14e598e61cfbe82269c3a354a5 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), @@ -29,4 +29,4 @@ sanity_check_paths = { 'dirs': [""], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 4ab3c4b882088688322a148927a4bae7ce718c7b..e138adfe4c6b7496064bccfb7ca248be6d4c0366 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -19,7 +19,7 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 355e0eb0ad04f64903e2d076425ac06aa09873d3..af291cd25c46c9ada3c7e5365a6a760e46e7bb4b 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -19,7 +19,7 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef8197538da889d177f6306c1e7f16992ea21b36 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb @@ -0,0 +1,38 @@ +# 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 +# Author: Jens Timmerman, Ghent University + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/taco/taco-0.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/taco/taco-0.5.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..833d9ac2f4792137b87f18e92e2fb2a00e116e25 --- /dev/null +++ b/easybuild/easyconfigs/t/taco/taco-0.5.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'taco' +version = '0.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://tacorna.github.io' +description = """Multi-sample transcriptome assembly from RNA-Seq""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/tacorna/taco/archive'] + +dependencies = [ + ('Python', '2.7.12'), +] + +postinstallcmds = ["mv %(installdir)s/bin/taco_run.py %(installdir)s/bin/taco_run"] + +sanity_check_paths = { + 'files': ['bin/taco_run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ba2836ed49288b02466f398e82c5ae0bf51ed25 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +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': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), +] + +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-5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..0eff73d3ccb746a330deb7df1086f2ade67b4430 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '5.2' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +osdependencies = ['texlive'] + +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 += "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 += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf', 'texmf/tex/texinfo/texinfo.tex'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae9bb8dae339bb4e1645b655c6788dd4d7f8a06a --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.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 = '2.2.20' + +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': '2016b'} +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/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 2a6923ac23c1a42426ae319856899c712eeb43c4..5cd635730b77cabde5904f022c980fb2bca1d5dd 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -12,17 +12,34 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code -sources = [SOURCELOWER_TAR_GZ] +sources = ['vasp.5.4.1.24Jun15.tar.gz'] + +# uncommment after downloading patches from http://cms.mpi.univie.ac.at/wiki/index.php/Installing_VASP +#patches = [ +# 'vasp.5.4.1.08072015.patch', +# 'vasp.5.4.1.27082015.patch', +# 'vasp.5.4.1.06112015.patch', +#] + +checksums = [ + '9a56174e272ac0c07645c42932848788', # vasp.5.4.1.24Jun15.tar.gz + 'ee242452bba6bb37459745f4617649d7', # vasp.5.4.1.08072015.patch + 'b137eb13804a60df382e77495dc738f9', # vasp.5.4.1.27082015.patch + 'd64b8f0ae861db7a76e6e9c9ffa188a1', # vasp.5.4.1.06112015.patch +] prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' # path to libfftw3xf_intel.a is hardcoded in makefile.include prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' +# remove mkl flag to prevent mixing dynamic libs with the static libs in LIBBLACS/SCALAPACK +prebuildopts += 'sed -i "s|-mkl||" makefile.include && ' + # VASP uses LIBS as a list of folders prebuildopts += 'unset LIBS && ' -buildopts = 'all BLACS="$LIBBLACS" ' +buildopts = 'all BLACS="$LIBBLACS" SCALAPACK="$LIBSCALAPACK"' parallel = 1 diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..d63c30f413e02bc7aee49f60fc002f0416053ddd --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,59 @@ +## +# 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': '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', '3.6.1')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', '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-7.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ce85c69cbd2c83caca5a2cbc964ffd084547a65d --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-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 = '7.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': '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', '3.6.1')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', 'mkg3states']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017.eb b/easybuild/easyconfigs/v/VTune/VTune-2017.eb new file mode 100644 index 0000000000000000000000000000000000000000..13d248cd6c44da89789aee3ea9c7f320896a94df --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017.eb @@ -0,0 +1,14 @@ +name = 'VTune' +version = '2017' + +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'] + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..722868d4b77ecc150db2b390a59d14a571a47ad6 --- /dev/null +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb @@ -0,0 +1,50 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = 'VampirTrace' +version = '5.14.4' + +homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' +description = """VampirTrace is an open source library that allows detailed logging of program + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] + +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), +] + +configopts = 'MPIFC="$MPIF90"' + +# MPI suite should always be specified -- MUCH quicker and SAVER than autodetect +# note: these options are toolchain specific! +configopts += " --with-openmpi --enable-compinst=gnu" + +configopts += " --with-papi-dir=${EBROOTPAPI}" +configopts += " --with-extern-otf-dir=${EBROOTOTF}" +configopts += " --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor" +configopts += " --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse" +configopts += " --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse" +configopts += " --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse" +# VamoirTrace does also support CUDA measurements - not yet tested +# configopts += " --with-cuda-dir=${CUDADIR}" + +sanity_check_paths = { + 'files': ['bin/vtcc', 'include/vampirtrace/vt_user.h', ('lib/libvt.a', 'lib64/libvt.a')], + 'dirs': [] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d08f6ddb122edca18046c54af57db35eceeb6291 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.3' + +homepage = "http://csg.sph.umich.edu/kang/verifyBamID/index.html" +description = """verifyBamID is a software that verifies whether the reads in particular file match previously known + genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of + two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When + external genotypes are not available, verifyBamID still robustly detects sample swaps. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['9b3d4c73c8f72e6b8f1e014702bc5bec'] + +buildopts = 'CXX="$CXX"' + +executables = ['%(name)s/bin/%(name)s'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch index f46ae78e872abdb14ebf9a038097c85d2782b2c3..baaf9b3859a573e919d5a7c7ed3397ccdd338e81 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch @@ -83,7 +83,7 @@ diff -ru WRFV3.orig/arch/postamble_new WRFV3/arch/postamble_new ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE NETCDFPATH = CONFIGURE_NETCDF_PATH -++NETCDFFPATH = CONFIGURE_NETCDFF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH HDF5PATH = CONFIGURE_HDF5_PATH WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH PNETCDFPATH = CONFIGURE_PNETCDF_PATH diff --git a/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..b18845a3b4540afc257c0fd731c72cd35edb0e20 --- /dev/null +++ b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +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': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/'] +sources = ['%(name)s-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), +] + +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/w/worker/worker-1.6.7-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f9fffe780440e11fc320abf2830391b2e08c000d --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.7' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +tcname = 'intel' +tcver = '2016b' +builddependencies = [(tcname, tcver)] +versionsuffix = '-%s-%s' % (tcname, tcver) + +exts_defaultclass = 'PerlModule' + +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'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), +] + +modextrapaths = { + 'PERL5LIB': ['share/perl5', 'lib64/perl5'], +} + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (tcname, tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ddb87ab0aa6a7c393a5ae8cd415f97130ecf2ea6 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +dependencies = [ + ('Python', '2.7.11'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('LibTIFF', '4.0.6'), + ('expat', '2.1.1'), + ('GTK+', '2.24.30'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('libSM', '1.2.2'), + ('libXxf86vm', '1.1.4'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..73dad53861834a289c25899929ade0889b9f75a4 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,34 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +patches = ['%(name)s_%(version)s_intel.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('libpng', '1.6.24'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('expat', '2.2.0'), + ('GTK+', '2.24.31'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c44e65c206b3e505bc4a5ff5630443c0a5d0c474 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb @@ -0,0 +1,131 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20160819' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] +dependencies = [ + ('freetype', '2.6.5'), + ('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-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index f735807177d3b0b4d4668a09daf47444a4713d19..556bda9f6eb6ed8d8e21799201a95af3ac63ddd5 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -23,6 +23,8 @@ builddependencies = [ dependencies = [ ('freetype', '2.6.5'), ('fontconfig', '2.12.1'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] default_easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..4359ea417ded3cc94d05d4f3a2870362cba8f8a9 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '0.6a2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +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 = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4be4224b10265396e54fe9274143ae80dd56d62 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '0.6a2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7ce4573e1fcc8f6b2e432058a7c65afc5786236 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44_01' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.24.0'), + ('expat', '2.2.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2179e09197bdb881ba0c926ea8bd3402ea473344 --- /dev/null +++ b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XMLStarlet' +version = '1.6.1' + +homepage = 'http://xmlstar.sourceforge.net' +description = """Command line XML tool""" + + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/xmlstar/files/%s/%s' % (name.lower(), version), 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libxslt', '1.1.28') +] + +sanity_check_paths = { + 'files': ['bin/xml', 'share/doc/xmlstarlet/html.css', 'share/doc/xmlstarlet/xmlstarlet-ug.html', + 'share/doc/xmlstarlet/xmlstarlet.txt', 'share/man/man1/xmlstarlet.1'], + 'dirs': ['bin', 'share/doc/xmlstarlet', 'share/man/man1'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..552256c88b4de49de7e6746016170c8f9bf4baa5 --- /dev/null +++ b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XMLStarlet' +version = '1.6.1' + +homepage = 'http://xmlstar.sourceforge.net' +description = """Command line XML tool""" + + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = [('http://sourceforge.net/projects/xmlstar/files/%s/%s' % (name.lower(), version), 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxml2', '2.9.2'), + ('libxslt', '1.1.28') +] + +sanity_check_paths = { + 'files': ['bin/xml', 'share/doc/xmlstarlet/html.css', 'share/doc/xmlstarlet/xmlstarlet-ug.html', + 'share/doc/xmlstarlet/xmlstarlet.txt', 'share/man/man1/xmlstarlet.1'], + 'dirs': ['bin', 'share/doc/xmlstarlet', 'share/man/man1'] +} + +moduleclass = 'data' 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 new file mode 100644 index 0000000000000000000000000000000000000000..9d2ac5e32d44e621e49d56164e86f9db15a1115a --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..cafe4d07ac58e87a7980efcc43775a3d677e8d8a --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', '0.19.8', '', True), + ('binutils', '2.25'), +] + +# 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-foss-2015a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb index 049e77b657e28521b59296523e4602205a7156a7..0245b4d8131971901d247b30a294dfc52595f32b 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.4'), + ('gettext', '0.19.4', '', True), ] # may become useful in non-x86 archs 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 new file mode 100644 index 0000000000000000000000000000000000000000..6d7bd28197966b53510dd70ed5278e4043151838 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2016.04'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +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-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 17cd0492c014a002a57767793e2e9dc0b16731fe..b4a5a18d700cf2816048b4b848003be504777041 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 @@ -11,15 +11,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -builddependencies = [ - ('Autotools', '20150215'), -] - gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver -dependencies = [ - ('gettext', gettext_ver), +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', gettext_ver, '', True), ] # may become useful in non-x86 archs 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 2a89ca6af63efcce64d992e231e493b084028ad7..9cb0eb5b874361d77d36bcfe071b544ca267ce7f 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.6'), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs 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 cd789593239335725ce2511e551d50c004eec3fb..8bddb8fe4aa2ea97f74854fe9259dc4a350b842b 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.8'), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs 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 f9a06be7327fdd83b568218cf5f373b55f036b03..c463ba319e13c74c4efaf04d242c994c87ea0fab 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), -] - -dependencies = [ - ('gettext', '0.18.2'), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs 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 96fe0ea8c8c03e8130eb5b4fcc2ae898df67f484..3e8e48f7606c1a4ab731c10dc9485a28bd7d1e8b 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.18.2'), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs 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 7953b85916795e46aa34d2a65a277b4d394b939b..b10cbfb5b1504ad1f766a29bc3d599032f8d98cf 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 @@ -11,15 +11,12 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -builddependencies = [ - ('Autotools', '20150215'), -] - gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver -dependencies = [ - ('gettext', gettext_ver), +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', gettext_ver, '', True), ] # may become useful in non-x86 archs 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 b717af018aaf06fa298f64daca32824917cf202c..e582d9cc6b8b36de8b63ae171fe513df8abdae3a 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.6'), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs 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 f05bff12d4debfc1b5b08501538c3555f8a78222..7d1af0e121bc515cd500a642e0926d8f963c08a1 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 @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.8'), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..25aeefc81ac57e31b262d17e734e465391695f7d --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160304' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://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/x265/x265-1.9-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..f346f0f6b3637fa340bb68a88f9aa8481f8b8b80 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '1.9' + +homepage = 'http://www.videolan.org/developers/x265.html' +description = """x265 is a free software library and application for encoding video streams into the H.265 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://ftp.videolan.org/pub/videolan/x265/'] +sources = ['x265_%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.5.2') +] +dependencies = [ + ('Yasm','1.3.0'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..abb82d5158e70dcfcccb4a0b3cc7c64d5a1b6967 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f011afc6c3c3bf289f13793b4c16cbce64bc8eab --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index 04fcdaad37b693c3506404ababea2fc09e0faaac..8cae54960cb52416522e68c105fbc1d514594fe8 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -11,6 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. @@ -21,21 +22,15 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.cpan.org/modules/by-module/YAML'] sources = [SOURCE_TAR_GZ] -perl = 'Perl' -perlver = '5.16.3' -perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) - dependencies = [ - (perl, perlver, perlverextra), + ('Perl', '5.16.3'), ] options = {'modulename': 'YAML::Syck'} -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/YAML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 4816f11ffde9ba24fff14f92533d7e3eed70c406..19442cc19e0b9528b10c19741b06037afb596f12 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -11,6 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. @@ -21,21 +22,15 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://www.cpan.org/modules/by-module/YAML'] sources = [SOURCE_TAR_GZ] -perl = 'Perl' -perlver = '5.16.3' -perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) - dependencies = [ - (perl, perlver, perlverextra), + ('Perl', '5.16.3'), ] options = {'modulename': 'YAML::Syck'} -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/YAML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2016b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2e871aa138cc75be19684e1e63d021a8b86091d --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.5.1' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://www.dkrz.de/redmine/attachments/download/473/'] +checksums = [('md5', '2176c5b1096146e58163656b9d83c0b3')] + +sanity_check_paths = { + 'files': ["include/yaxt.h", "include/yaxt.mod", "lib/libyaxt.a", "lib/libyaxt.%s" % SHLIB_EXT], + 'dirs': ["include/xt"], +} + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..c741427654e368addf892cfcdb31fae2bd2b0cf0 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '2016.06a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Yade-%(version)s_include-signal.patch'] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('CGAL', '4.8.1', versionsuffix), + ('GDB', '7.11.1', versionsuffix), + ('GL2PS', '1.3.9'), + ('GTS', '0.7.6'), + ('IPython', '5.1.0', versionsuffix), + ('libQGLViewer', '2.6.3'), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.2', versionsuffix), + ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.12'), + ('Qt5', '5.7.0'), + ('SQLite', '3.13.0'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Eigen', '3.2.9'), +] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$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')], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch b/easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch new file mode 100644 index 0000000000000000000000000000000000000000..28ff927ab481675a054d9f038bbe746d4ae0ef1f --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch @@ -0,0 +1,10 @@ +--- trunk-2016.06a/py/wrapper/yadeWrapper.cpp.orig 2016-09-06 20:32:45.079249073 +0200 ++++ trunk-2016.06a/py/wrapper/yadeWrapper.cpp 2016-09-06 20:32:59.049059903 +0200 +@@ -39,6 +39,7 @@ + + #include + #include ++#include + + namespace py = boost::python; + diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..09279b532af233dab2248c5a4de6dd5e2a36e5e7 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = "Yasm-1.3.0: Complete rewrite of the NASM assembler with BSD license" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb index 1c29958289a7b9c07c17e230605aeec2acec2e60..1192872c10316dd3162a345a2deafeccbff72486 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb @@ -9,6 +9,7 @@ not covered by any patents -- lossless data-compression library for use on virtu computer hardware and operating system.""" toolchain = {'name': 'GCC', 'version': '4.7.3'} +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-GCC-4.8.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7207b104ac81c47f841044ce1fe18aeb5883f7b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb @@ -0,0 +1,22 @@ +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': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +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-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..47a40a40359f1496c3ff7f56ad0b42f38f431d46 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -0,0 +1,25 @@ +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': '6.1.0'} +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/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..a484ded00032b5acc48fe71d67dec73ce98e6f6f --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb @@ -0,0 +1,22 @@ +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +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-iomkl-2016.07.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..5afd211f68b447080ffde7255a2c9d4c7549360d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..66cf47a99cf3a71949c09fbce1c07ffa1e367c89 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +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.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb index 82a1155e2efd8f23e8967a8d05e2b73f27a7d868..ec9d1a0bdf681af40176ee0ea36106c33e0c6af2 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb @@ -9,6 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/setup.py b/setup.py index c52c2d05501f429d0fdbd539c21e16c349563652..003be273e747d695c2b9d71922a2b631d02e61ea 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.9.0.dev0' +VERSION = '3.1.0.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 13ea1263cd83ad9b50f5e61f9fef253c7af056ca..5901ae8d4cf48e302731cc340500e8254322fbcd 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -44,9 +44,10 @@ import easybuild.main as main import easybuild.tools.options as eboptions from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.easyconfig import EasyConfig -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class -from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for, resolve_template +from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config from easybuild.tools.config import build_option @@ -168,11 +169,11 @@ class EasyConfigTest(TestCase): def test_easyconfig_locations(self): """Make sure all easyconfigs files are in the right location.""" - easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[a-z]/[^/]+$') + easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) for (dirpath, _, filenames) in os.walk(topdir): - # ignore git/svn dirs - if '/.git/' in dirpath or '/.svn/' in dirpath: + # ignore git/svn dirs & archived easyconfigs + if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue # check whether list of .eb files is non-empty easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] @@ -210,7 +211,7 @@ def template_easyconfig_test(self, spec): name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) # make sure easyconfig file is in expected location - expected_subdir = os.path.join('easybuild', 'easyconfigs', name.lower()[0], name) + expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) self.assertEqual(expected_subdir, subdir, fail_msg) @@ -258,7 +259,8 @@ def template_easyconfig_test(self, spec): self.assertTrue(os.path.isfile(ext_patch_full), msg) # check whether all extra_options defined for used easyblock are defined - for key in app.extra_options(): + extra_opts = app.extra_options() + for key in extra_opts: self.assertTrue(key in app.cfg) app.close_log() @@ -269,7 +271,7 @@ def template_easyconfig_test(self, spec): os.close(handle) ec.dump(test_ecfile) - dumped_ec = EasyConfig(test_ecfile) + dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() os.remove(test_ecfile) # inject dummy values for templates that are only known at a later stage @@ -278,10 +280,24 @@ def template_easyconfig_test(self, spec): 'installdir': '/dummy/installdir', } ec.template_values.update(dummy_template_values) - dumped_ec.template_values.update(dummy_template_values) - for key in sorted(ec._config): - self.assertEqual(ec[key], dumped_ec[key]) + ec_dict = ec.parser.get_config_dict() + keys = [] + for key in ec_dict: + # skip parameters for which value is equal to default value + orig_val = ec_dict[key] + if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: + continue + if key in extra_opts and orig_val == extra_opts[key][0]: + continue + if key not in DEFAULT_CONFIG and key not in extra_opts: + continue + + keys.append(key) + orig_val = resolve_template(ec_dict[key], ec.template_values) + dumped_val = resolve_template(dumped_ec[key], ec.template_values) + + self.assertEqual(orig_val, dumped_val) # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) @@ -289,6 +305,7 @@ def template_easyconfig_test(self, spec): # test passed, so set back to True single_tests_ok = True and prev_single_tests_ok + def suite(): """Return all easyblock initialisation tests.""" # dynamically generate a separate test for each of the available easyconfigs @@ -296,6 +313,11 @@ def suite(): easyconfigs_path = get_paths_for('easyconfigs')[0] cnt = 0 for (subpath, _, specs) in os.walk(easyconfigs_path, topdown=True): + + # ignore archived easyconfigs + if '__archive__' in subpath: + continue + for spec in specs: if spec.endswith('.eb') and spec != 'TEMPLATE.eb': cnt += 1